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PDB ID Mentions in PubMed Central Article count: 58

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PDB ID Mentions in PubMed Central

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Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins.

(2006) BMC Bioinformatics 7

PubMed: 16597327 | PubMedCentral: PMC1523218 | DOI: 10.1186/1471-2105-7-189

We list the PDB code, the name of the protein and the number of the transmembrane segments PDB code Name Number of transmembrane segments 1RC2 :B AQUAPORIN Z 6 1J4N :A AQUAPORIN 1 6 1IWG :A MULTIDRUG ... FFLUX TRANSPORTER ACRB 12 1NEK :C SUCCINATE DEHYDROGENASE CYTOCHROME B-556 SUBUNIT 3 1NEK :D SUCCINATE_DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN 3 1Q16 :C RESPIRATORY NITRATE REDUCTASE 1 GAMMA CHAIN 5 1RH5 :B PREPROTEIN TRANSLOCASE SECE SUBUNIT 1 1RH5 :C PREPROTEIN TRANSLOCASE SECBETA SUBUNIT 1 1IZL :A PHOTOSYSTEM II SUBUNIT PSBA 5 1IZL :C PHOTOSYSTEM II SUBUNIT PSBC 5 1YCE ROTOR OF F-TYPE NA+-ATPASE 2 2BL2 ROTOR OF V-TYPE NA+-ATPASE 4 1XQF :A PROBABLE AMMONIUM TRANSPORTER 11 1KPL :A H+/CL- EXCHANGE TRANSPORTER 14 1S5L :B PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN 6 1S5L :C PHOTOSYSTEM II CP43 PROTEIN 6 1S5L :D PHOTOSYSTEM II REACTION CENTER D2 PROTEIN 5 1S5L :E CYTOCHROME B559 ALPHA SUBUNIT 1 1FX8 :A GLPF GLYCEROL FACILITATOR CHANNEL 6 1LNQ :A MTHK POTTASIUM CHANNEL, CA-GATED 2 1MXM :A MECHANOSENSITIVE CHANNEL PROTEIN 3 1Q90 :M CYTOCHROME B6F COMPLEX SUBUNIT PETM 1 1VF5 :C CYTOCHROME F 1 1K4C :C POTASSIUM CHANNEL KCSA 2 1ZCD :A NA(+)/H(+) ANTIPORTER 1 12 2A79 :B POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 2 6

Publication Year: 2006


Prediction of transmembrane helix orientation in polytopic membrane proteins.

(2006) BMC Struct Biol 6

PubMed: 16792816 | PubMedCentral: PMC1540425 | DOI: 10.1186/1472-6807-6-13

The PDB names for the protein structures used: 1C3W , 1E12 , 1EHK , 1EUL , 1FX8 , 1H2S , 1IWG , 1J4N , 1JB0 , 1K4C , 1KB9 , 1KF6 , 1KPL , 1KQF , 1L7V , 1L9H , 1M3X , 1M56 , 1MSL , 1NEK , 1OCR , 1OKC ,... 1PP9 , 1PV6 , 1PW4 , 1Q16 , 1QLA , 1Q90 , 1RH5 .

Publication Year: 2006


Status of the intracellular gate in the activated-not-open state of shaker K+ channels.

(2005) J Gen Physiol 126

PubMed: 16260836 | PubMedCentral: PMC1794167 | DOI: 10.1085/jgp.200509385

A potassium ion with eight waters of hydration based on the high-resolution structure of KcsA ( Zhou et al., 2001b ; Protein Data Bank entry 1K4C) is shown in the cavity for reference.

Publication Year: 2005


Structural and thermodynamic properties of selective ion binding in a K+ channel.

(2007) PLoS Biol 5

PubMed: 17472437 | PubMedCentral: PMC1858713 | DOI: 10.1371/journal.pbio.0050121

(B) This conductive K + structure is from PDB 1K4C.

The structures were solved by molecular replacement using the high K + KcsA-Fab structure (Protein Data Bank (PDB)code 1K4C) as a search model in molrep [ 29 ].

Amino acids E71 to D80 are shown in a stick diagram (from PDB 1K4D and PDB 1K4C) encompassing the selectivity filter (T75-G79) and surrounding residues.

Publication Year: 2007


Anti-calmodulins and tricyclic adjuvants in pain therapy block the TRPV1 channel.

(2007) PLoS One 2

PubMed: 17579717 | PubMedCentral: PMC1890308 | DOI: 10.1371/journal.pone.0000545

The X-ray crystal structure of the M1-pore loop-M2 of the KcsA was used (PDB accession code 1K4C) as a template for homology modeling.

Publication Year: 2007


A cation-pi interaction between extracellular TEA and an aromatic residue in potassium channels.

(2006) J Gen Physiol 128

PubMed: 17130518 | PubMedCentral: PMC2151593 | DOI: 10.1085/jgp.200609654

Specifically, the side chain of Tyr82 in many published structures of KcsA (e.g., 1BL8 [ Doyle et al., 1998 ], 1K4C [ Zhou et al., 2001 ], 1R3J [ Zhou and MacKinnon, 2003 ], 2A9H [ Yu et al., 2005 ], ... nd 1ZWI [ Cordero-Morales et al., 2006 ]; in the Protein Data Bank [ www.rcsb.org/pdb/ ]) is aligned such that a TEA positioned to block the channel would not interact with the face of the aromatic ring ( Fig. 1 , blue side chains).

Publication Year: 2006


Structural determinants of the closed KCa3.1 channel pore in relation to channel gating: results from a substituted cysteine accessibility analysis.

(2007) J Gen Physiol 129

PubMed: 17353352 | PubMedCentral: PMC2151617 | DOI: 10.1085/jgp.200609726

Computer-based Homology Modeling The closed KCa3.1 channel model structure was produced by automated homology modeling using Modeller v7.0 and involved the generation of 150 models using KcsA (PDB 1K4... ) as template ( Sali and Blundell, 1993 ).

Publication Year: 2007


Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels.

(2007) J Gen Physiol 129

PubMed: 17227917 | PubMedCentral: PMC2154357 | DOI: 10.1085/jgp.200609633

TABLE I Calculated ΔΔG (in kcal/mol) for the Binding Sites of KcsA and NaK Site KcsA (1K4C) KcsA (1BL8) NaK S0 −1.3 −1.1 S1 2.6 (2.1) 2.8 S2 5.3 (4.8) 6.6 −0.9 ... −1.1) S3 1.8 (2.7) 2.4 1.1 (1.7) S4 −1.2 −1.5 −0.9 Cavity −0.8 −0.2 −0.6 The calculations on the KcsA channel were done for the x-ray structures 1K4C ( Noskov et al., 2004 ) and 1BL8 ( Bernèche and Roux, 2001 ) using the CHARMM PARAM27 force field ( MacKerell et al., 1998 ).

Publication Year: 2007


Intrinsic electrostatic potential in the BK channel pore: role in determining single channel conductance and block.

(2008) J Gen Physiol 131

PubMed: 18227273 | PubMedCentral: PMC2213566 | DOI: 10.1085/jgp.200709862

Online Supplemental Material In the supplemental material (available at http://www.jgp.org/cgi/content/full/jgp.200709862/DC1 ) the model for the human BK pore built using the crystallographic data fo... KcsA channel (PDB:1K4C) and MthK channel (PDB:1LNQ) as structural references is described in detail.

The model for the human BK pore was built using the primary sequence read from Gene Bank (GI:46396283) and the crystallographic data for KcsA channel (K + channel from Streptomyces lividans ; PDB:1K4C) and MthK channel (PDB:1LNQ) as structural references.

Publication Year: 2008


On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation.

(2004) J Gen Physiol 124

PubMed: 15572347 | PubMedCentral: PMC2234034 | DOI: 10.1085/jgp.200409111

The selectivity filter of the KcsA potassium channel, PDB:1K4C ( Zhou et al., 2001 ), for example, exhibits temperature factors B = 8π 2 〈Δ r 2 〉/3 on the order of 15&#... 02013;20 Å 2 at liquid nitrogen temperature 140 K, corresponding to RMS fluctuations of at least 0.75 Å.

Fig. 8 shows the potential profile calculated for the 3.2 Å PDB:1BL8 ( Doyle et al., 1998 ) and 2.0 Å PDB:1K4C ( Zhou et al., 2001 ) resolution KcsA potassium channel structures.

Potential energy profiles for the 3.2 Å resolution PDB:1BL8 (- -) and 2.0 Å resolution PDB:1K4C (—) KcsA potassium channel structures.

Publication Year: 2004


Investigating the putative glycine hinge in Shaker potassium channel.

(2005) J Gen Physiol 126

PubMed: 16103276 | PubMedCentral: PMC2266578 | DOI: 10.1085/jgp.200509287

(A) Two opposing subunits of KcsA from a high-resolution crystal structure (1K4C; Zhou et al., 2001b ), highlighting the position of the pore-lining residue homologous to Val467 in Shaker (red... .

A high-resolution structure of KcsA (1K4C, 2.00 Å; Zhou et al., 2001b ) is shown in Fig. 10 B (left), along with the expected effect of the G99A mutation that introduces this steric clash in KcsA (right).

Publication Year: 2005


S1 constrains S4 in the voltage sensor domain of Kv7.1 K+ channels.

(2008) PLoS One 3

PubMed: 18398461 | PubMedCentral: PMC2275789 | DOI: 10.1371/journal.pone.0001935

The closed state To obtain the closed state, we first aligned the Kv7.1 open-state model with KcsA (PDB ID code 1K4C) by superposing the selectivity filter and the pore helix of the two structures, as... performed by Long et al [13] .

Publication Year: 2008


Cooperative transition between open and closed conformations in potassium channels.

(2008) PLoS Comput Biol 4

PubMed: 18769593 | PubMedCentral: PMC2528004 | DOI: 10.1371/journal.pcbi.1000164

Materials and Methods Structures Three structures of the homotetrameric channel were used: two of KcsA (PDB identifiers: 1bl8 [1] and 1k4c [38] ; Figure 1B ) and one of... MthK (PBB: 1lnq [2] ; Figure 2B ).

Results/Discussion We analyzed the two structures of the KcsA channel (PBD identifiers 1bl8 [1] and 1k4c [38] ; Figure 1B and 1E ) and the structure of the MthK channel (PDB identifier 1lnq [2] ; Figure 2B and 2E ).

Publication Year: 2008


Structural analysis of ion selectivity in the NaK channel.

(2009) Nat Struct Mol Biol 16

PubMed: 19098915 | PubMedCentral: PMC2615071 | DOI: 10.1038/nsmb.1537

a) Superimposition of the NaK selectivity filter (yellow) in complex with K + with that of KcsA (green, PDB code 1K4C).

Publication Year: 2009


High-resolution structure of the open NaK channel.

(2009) Nat Struct Mol Biol 16

PubMed: 19098917 | PubMedCentral: PMC2615073 | DOI: 10.1038/nsmb.1531

Superimposition of the closed NaK structure (red, PDB code 2AHY) with KcsA (yellow, PDB code 1K4C) viewed from the intracellular side along 4-fold axis and the equivalent superimposition of the open N... KNΔ19 structure (blue) with the MthK pore (orange, PDB code1LNQ) are shown.

Publication Year: 2009


PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.

(2009) PLoS Comput Biol 5

PubMed: 19609355 | PubMedCentral: PMC2704872 | DOI: 10.1371/journal.pcbi.1000440

(A) KirBac1.1 potassium channel (1p7b); (B) bovine aquaporin-1 (1j4n); (C) KcsA potassium channel (1k4c); (D) MthK calcium-gated potassium channel (1lnq); (E) CorA Mg 2+ transporter (2iub); (F... MscS voltage-modulated mechanosensitive channel (2oau); (G) ASIC1 acid-sensing ion channel (2qts); (H) SecYE-beta protein-conducting channel (2yxr); (I) Kv1.2 voltage-gated potassium channel (2a79); (J) sodium-potassium channel (2ahy); (K) Amt-1 ammonium channel (2b2f); (L) nicotinic acetylcholine receptor (2bg9).

Publication Year: 2009


Protein-protein docking using region-based 3D Zernike descriptors.

(2009) BMC Bioinformatics 10

PubMed: 20003235 | PubMedCentral: PMC2800122 | DOI: 10.1186/1471-2105-10-407

HEX ZDOCK LZerD Complex Rank lRMSD HITS2K Rank lRMSD HITS2K Rank lRMSD HITS2K 1ACB 694 8.3 3 185 9.98 5 21 9.98 2 1AHW 234 8 3 34 9.86 20 5 2.68 43 1AKJ 209 9.6 10 - - - - - - 1AVX 108 8.9 7 604 9.43 ... - - - 1AY7 645 9.9 4 568 9.39 11 1884 6.13 1 1B6C 593 9 2 182 5.6 10 73 6.2 10 1BUH 743 7.7 2 - - - 599 9.73 1 1BVK - - - 70 7.56 1125 9.83 10 1BVN 63 9.1 20 29 8.65 52 2 6.89 49 1CGI 42 9.4 17 145 3.88 32 86 8.13 12 1D6R 447 7.7 1 303 8.44 3 344 7.84 8 1DE4 946 8.6 1 - - - - - - 1DFJ 17 9.5 14 5 6.64 67 - - - 1DQJ - - - 152 9.82 23 - - - 1E6E 109 5.6 10 - - - 52 4.49 10 1E6J - - - 12 5.34 93 87 9.97 20 1E96 - - - - - - 1375 8.91 1 1EAW 9 5 20 3 5.43 87 6 9.95 19 1EER 609 9.2 8 - - - - - - 1EWY 76 9.1 12 22 8.08 51 103 9.91 110 1EZU - - - - - - 815 7.89 3 1F34 124 6.7 11 5 5.45 20 - - - 1F51 371 9.6 5 602 9.78 4 1101 8.31 1 1FQJ 41 8 12 - - - 1014 9.63 3 1FSK 5 1.8 16 1 4.04 149 15 6.23 28 1GHQ - - - - - - 1571 9.14 1 1GRN 914 9.1 2 1704 5.81 2 1407 7.41 2 1HE1 37 6.4 18 23 8.14 8 47 6.2 7 1HIA 51 8.7 6 - - - 1 9.49 74 1I4D - - - - - - 286 9.11 2 1I9R 82 2.1 8 104 9.07 16 104 9.41 10 1IJK 1012 8.7 3 - - - - - - 1IQD - - - 492 8.99 11 41 6.46 27 1JPS - - - 171 8.51 7 292 2.01 20 1K4C 21 9.6 1 - - - 219 9.78 6 1KAC 687 8.7 1 - - - 655 3.95 3 1KXP 36 9.4 13 1616 7.11 2 1226 8.05 1 1KXQ 488 7.1 5 116 7.58 29 73 4.33 16 1M10 514 9.5 2 - - - - - - 1MAH 2 1.2 20 92 3.86 9 92 2.43 2 1ML0 - - - 36 2.87 35 121 5.71 2 1MLC 408 3.6 2 110 6.17 12 1834 4.48 1 1NCA 116 1.2 5 14 7.08 49 270 9.97 2 1NSN 142 1.5 6 185 5.07 19 94 8.61 4 1PPE 2 9.7 47 1 0.86 358 1 2.26 184 1QA9 - - - - - - 546 8.07 6 1QFW - - - 257 8.63 4 108 9.54 2 1TMQ 356 5.9 9 314 6.12 11 50 3.71 11 1UDI 8 6.2 9 32 8.04 34 19 6.4 16 1VFB - - - 22 8.52 65 150 8.7 22 1WEJ - - - 81 8.36 42 156 9.82 18 1WQ1 125 7.1 10 610 9.9 5 32 9.79 11 2BTF - - - 553 6.39 3 - - - 2JEL 164 6 3 45 4.49 86 66 6.81 35 2MTA 136 9 4 - - - 4 7.57 48 2QFW - - - - - - 68 9.01 11 2SIC 57 8.8 8 173 8.62 18 127 4.59 6 2SNI 256 9.6 7 534 9.69 4 - - - 7CEI 61 8.7 5 106 7.11 28 - - - Summary HEX ZDOCK LZerD Mean 206 173 164 Rank<100 17 19 22 Rank<500 32 33 34 Rank<1000 42 39 38 Rank<2000 43 41 47 Win 18 20 22 The results of HEX are taken from the columns of "U-U shape-only Blind search" in Table 3 of the paper by Ritchie et al .

Original ZDOCK Rank Context Shapes (CS) PatchDock ZDOCK Decoys Reranked by LZerD Score LZerD Complex Rank a) iRMSD HIT2K Rank iRMSD RMSD iRMSD Rank iRMSD HIT2K Rank iRMSD HIT2K 1AHW 268 2.28 21 402 2.46 181 2.49 15 1.68 50 5 1.34 42 1AK4 - b) - - - - - - (NA NA NA) 43787 2.35 0 1AKJ 4872 2.29 0 - - - - 1985 1.93 1 - - - 1AVX 2863 2.23 0 - - - - 5689 2.22 0 786 2.41 2 1AY7 5584 1.33 0 - - - - 394 1.1 7 1884 1.98 1 1B6C 1717 2.43 2 - - - - 497 2.13 8 1001 2.41 1 1BJ1 129 0.86 49 1893 1.93 - - 306 1.01 20 298 1.86 7 1BUH 14556 2.37 0 - - - - 11230 2.42 0 12251 1.6 0 1BVK 3970 1.94 0 - - 2754 2.27 9560 2.43 0 5515 2.24 0 1BVN 502 1.97 13 34 2.34 - - 8 2.26 59 27 2.32 6 1CGI 145 2.44 9 - - 1120 2.11 1775 2.14 1 9041 2.1 0 1D6R 2951 2.03 0 - - - - 5022 2.49 0 2619 2.24 0 1DFJ 9 2.27 40 - - - - 9350 2.14 0 - - - 1DQJ 2287 2.48 0 - - - - 5391 2.32 0 20816 2.09 0 1E6E 22643 2.08 0 - - - - 432 1.94 2 52 2.13 8 1E6J 15 1.56 34 - - - - 2509 1.81 0 439 2.18 8 1E96 3094 2.26 0 - - - - 882 1.88 2 216 2.14 2 1EAW 3 1.54 62 94 2.29 85 2.29 5 1.48 111 20 2.42 10 1EWY 259 2.32 2 - - - - 1007 2.14 4 349 2.36 14 1EZU 1100 1.94 3 - - - - 589 1.42 4 824 1.21 2 1F34 5 2.2 13 - - 490 1.81 5082 1.61 0 - - - 1F51 230 2.18 4 - - - - 154 1.76 5 3545 1.58 0 1FQJ 9889 2.29 0 - - - - 628 2.39 2 - - - 1FSK 1 1.63 105 20 1.57 221 2.39 29 1.57 76 15 2.4 11 1GCQ 24339 2.29 0 - - - - 39221 2.29 0 9418 1.8 0 1GHQ - - - - - - - (NA NA NA) 15357 1.68 0 1GRN 1704 2.34 2 - - - - 1884 1.74 1 1407 2.18 1 1HE1 4672 1.31 0 1029 2.17 - - 51 2 8 267 1.98 2 1HIA - - - - - - - (NA NA NA) 44189 2.42 0 1I9R 50 2.45 41 - - - - 57 1.96 10 95 2.39 21 1IJK 52731 2.44 0 - - - - 39460 2.44 0 6731 2.45 0 1IQD 612 2.27 5 - - - - 36 0.99 27 41 1.2 18 1JPS 171 1.81 9 - - - - 5305 1.37 0 292 0.9 20 1K4C 20806 1.53 0 - - - - 4468 1.18 0 1188 1.43 7 1KAC 2896 2.33 0 - - - - 1313 2.33 1 655 2.18 3 1KTZ 53599 1.69 0 - - - - 33926 1.69 0 12162 1.19 0 1KXP 1734 2.36 1 - - - - 32023 1.91 0 14208 2.22 0 1KXQ 212 1.91 13 2226 1.73 - - 629 1.24 4 73 1.68 14 1MAH 92 1.31 9 597 1.16 887 2.28 541 0.89 6 92 0.87 2 1ML0 36 1.56 21 - - 231 2.02 406 1.37 6 559 2.38 3 1MLC 110 1.19 12 18 2.28 - - 243 1.07 12 1834 1.16 1 1NCA 14 1.93 47 - - - - 302 1.55 12 12528 1.5 0 1NSN 185 1.81 5 26 1.79 - - 147 1.81 13 945 2.29 1 1PPE 1 0.57 218 2 2.31 - - 1 0.72 194 1 0.83 68 1QA9 5672 1.88 0 - - - - 5924 1.82 0 1381 2.19 3 1QFW 257 1.14 7 597 1.73 - - 136 2.31 17 108 1.24 4 1RLB - - - - - - - (NA NA NA) 46073 1.24 0 1TMQ 314 1.88 11 783 1.68 1 1.96 90 1.45 19 50 1.45 5 1UDI 258 2.17 4 2649 2.14 27 2.42 219 2.39 3 59 2.36 6 1VFB 2734 1.79 0 228 2.46 - - 1534 1.61 1 1303 1.69 1 1WEJ 465 2.37 8 - - - - 916 1.97 1 3914 2.06 6 1WQ1 1101 2.49 2 - - - - 284 2.05 2 141 1.87 2 2JEL 45 1.79 33 - - - - 149 2.44 19 133 2.49 9 2MTA - - - - - 515 2.19 (NA NA NA) 606 1.64 11 2PCC - - - - - - - (NA NA NA) 4542 2.31 0 2QFW 832 2.29 3 33 2.32 - - 42 1.99 17 68 1.55 29 2SIC 173 1.86 24 1077 2.28 - - 17 1.85 61 12 2.04 9 2SNI 17906 2.44 0 - - - - 428 2.33 2 - - - 7CEI 106 1.97 24 2290 1.9 366 1.07 705 1.57 7 6765 2.03 0 Summary c) ZDOCK CS PatchDock (PD) LZerD Rerank LZerD Rank<100 11 7 3 11 14 Rank<500 26 9 6 26 23 Rank<1000 29 12 9 32 29 Rank<2000 33 15 10 38 36 Wins vs. LZerD Rerank ZDOCK/LZerD Rerank 26/26 CS/LZerD Rerank 5/34 PD/LZerD Rerank 7/34 - - Wins vs. LZerD ZDOCK/LZerD 24/33 CS/LZerD 5/34 PD/LZerD 8/34 LZerD Rerank/LZerD 24/28 - LZerD results are compared with ZDOCK, Context Shapes, and PatchDock.

Publication Year: 2009


Inactivation of the KcsA potassium channel explored with heterotetramers.

(2010) J Gen Physiol 135

PubMed: 20038524 | PubMedCentral: PMC2806417 | DOI: 10.1085/jgp.200910305

Superposition of the selectivity filter region of the WT KcsA structure (PDB entry 1K4C; magenta) and the flipped E71A KcsA structure (PDB entry 2ATK; green).

Superimposition of the KcsA crystal structure (PDB entry 1K4C) with the crystal structures of the K v 1.2 channel from the Shaker family (PDB entries 2A79 and 2R9R) and the KvAP channel (PDB entry 1ORQ) suggests that in these channels there also exist networks of interactions between the pore helix and the external entrance of the channel.

Publication Year: 2010


An electrostatic interaction between TEA and an introduced pore aromatic drives spring-in-the-door inactivation in Shaker potassium channels.

(2009) J Gen Physiol 134

PubMed: 19917730 | PubMedCentral: PMC2806421 | DOI: 10.1085/jgp.200910260

(A) KcsA crystal structure with Y82 shown in space filling representation; PDB, 1K4C.

Publication Year: 2009


On the functional significance of soft modes predicted by coarse-grained models for membrane proteins.

(2010) J Gen Physiol 135

PubMed: 20513758 | PubMedCentral: PMC2888054 | DOI: 10.1085/jgp.200910368

1K4C ) and Glt Ph (PDB accession no.

Publication Year: 2010


Novel insights into K+ selectivity from high-resolution structures of an open K+ channel pore.

(2010) Nat Struct Mol Biol 17

PubMed: 20676101 | PubMedCentral: PMC2918291 | DOI: 10.1038/nsmb.1865

( d ) Superimposition of the selectivity filter of MthK (grey) and KcsA (gold, PDB code 1K4C).

The structures were determined by molecular replacement using AMoRe in the CCP4 suite 28 using KcsA structure (PDB code 1K4C) as an initial search model followed by repeated cycles of model building with XtalView 29 and refinement with REFMAC 28 .

Publication Year: 2010


n-->pi* interactions in proteins.

(2010) Nat Chem Biol 6

PubMed: 20622857 | PubMedCentral: PMC2921280 | DOI: 10.1038/nchembio.406

Figure 5 Potential n → π * interactions in the selectivity filter of the KcsA potassium ion channel A single chain of the tetrameric channel determined at a high K + concentration (PDB... code 1k4c) structure was superposed on that determined at a low K + concentration (PDB code 1k4d).

Publication Year: 2010


Residues at the tip of the pore loop of NR3B-containing NMDA receptors determine Ca2+ permeability and Mg2+ block.

(2010) BMC Neurosci 11

PubMed: 20958962 | PubMedCentral: PMC2974739 | DOI: 10.1186/1471-2202-11-133

Homology modeling and molecular dynamics simulations NR1-3a and NR3B homology models were created based on the KcsA structure (1k4c) Several individual modeling steps using YASARA Structure (version 9... 10.5) were required [ 22 ].

Publication Year: 2010


On the structural basis of modal gating behavior in K(+) channels.

(2011) Nat Struct Mol Biol 18

PubMed: 21186363 | PubMedCentral: PMC3059741 | DOI: 10.1038/nsmb.1968

( a ) Single-subunit line representation of the P-loop of E71I overlaid onto the wt structure 5 (PDB entry 1K4C ) highlights the conductive conformation of the selectivity filter backbone.

( a ) Single-subunit line representation of the P-loop of E71Q overlaid onto the wt structure 5 (PDB entry 1K4C ) highlights the conductive conformation of the selectivity filter backbone.

Crystallographic analysis Structures were solved by molecular replacement using only the Fab fragment and extracellular part of wt KcsA (PDB 1K4C) without the selectivity filter as a search model to reduce the biasing of model prediction, as the expected conformation is supposed to be different from the closed state.

Crystals of mutants E71I and E71Q were obtained as Fab complexes, diffracting at resolutions of 2.3 Å and 2.7 Å, respectively, and were solved by molecular replacement methods 5 using the structure of wt KcsA (1K4C) as search model.

4 and 5 ) showed no major changes in backbone conformation and thus, corresponds to the conductive conformation of the filter observed in most closed KcsA structures (RMSD with respect to 1K4C is 0.25 Å for E71I and 0.12 Å for E71Q).

Publication Year: 2011


A specific two-pore domain potassium channel blocker defines the structure of the TASK-1 open pore.

(2011) J Biol Chem 286

PubMed: 21362619 | PubMedCentral: PMC3077598 | DOI: 10.1074/jbc.M111.227884

Molecular Modeling Based on the crystal structures of KcsA and KvAP (PDB IDs 1K4C and 1ORQ , respectively), homology models of TASK-1 were created using the Modeler 7 version 7 software.

Publication Year: 2011


Origins of ion selectivity in potassium channels from the perspective of channel block.

(2011) J Gen Physiol 137

PubMed: 21518829 | PubMedCentral: PMC3082928 | DOI: 10.1085/jgp.201010551

1K4C ) with only two opposing subunits shown for clarity: the carbonyl oxygens forming the K + -binding sites in the selectivity filter (S0–S4) in red and K + ions in purple.

1K4C ); (B) high Na + and no K + ( Zhou et al., 2001 ) (Protein Data Bank accession no.

Publication Year: 2011


A combination of compositional index and genetic algorithm for predicting transmembrane helical segments.

(2011) PLoS One 6

PubMed: 21814556 | PubMedCentral: PMC3144211 | DOI: 10.1371/journal.pone.0021821

For example, the pore (P) helix of the potassium channel KcsA (1K4C) and the nitropropionic acid (NPA) contain loops of the aquaporins.

Publication Year: 2011


Benchmarking and analysis of protein docking performance in Rosetta v3.2.

(2011) PLoS One 6

PubMed: 21829626 | PubMedCentral: PMC3149062 | DOI: 10.1371/journal.pone.0022477

PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification 1K74 rigid-body ... O 2 2.5 [1.1] 0.20 1.63 RB sampling 1EER difficult | O 1 0.9 [1.0] 0.02 2.23 BB sampling 1Z5Y rigid-body | O 2 2.4 [1.1] 0.16 1.14 BB sampling 1FAK difficult | O 1 0.9 [0.9] 0.01 3.30 discrimination 1WEJ rigid-body | A 2 2.2 [1.1] 0.14 2.60 discrimination 1TMQ rigid-body | E 1 0.8 [0.9] 0.01 1.47 RB sampling 1HE8 medium | O 2 2.2 [1.1] 0.13 3.19 BB sampling 1I4D rigid-body | O 1 0.8 [0.9] 0.01 3.13 RB sampling 1ATN difficult | O 2 2.1 [1.2] 0.12 1.53 RB sampling 1RLB rigid-body | O 1 0.8 [0.9] 0.01 3.88 RB sampling 2HQS rigid-body | O 2 2.1 [1.2] 0.13 2.69 BB sampling 1Z0K rigid-body | O 1 0.7 [0.8] 0.00 3.56 BB sampling 1JMO difficult | O 2 2.1 [1.2] 0.11 2.82 BB sampling 1EFN rigid-body | O 1 0.7 [0.8] 0.00 3.58 BB sampling 2O8V rigid-body | E 2 2.1 [1.2] 0.12 3.62 BB sampling 1I9R rigid-body | AB 1 0.6 [0.8] 0.00 0.52 RB sampling 1J2J rigid-body | O 2 2.0 [1.4] 0.14 1.10 BB sampling 1AZS rigid-body | O 0 0.5 [0.9] 0.01 5.41 RB sampling 1NSN rigid-body | AB 2 2.0 [1.2] 0.10 1.15 discrimination 2B42 rigid-body | E 0 0.4 [0.6] 0.00 5.85 RB sampling 1K5D medium | O 2 2.0 [1.1] 0.09 2.87 BB sampling 2BTF rigid-body | O 0 0.3 [0.6] 0.00 4.44 BB sampling 1FQ1 difficult | E 2 1.7 [1.3] 0.08 2.18 RB sampling 1KKL medium | E 0 0.2 [0.5] 0.00 4.60 RB sampling 2AJF rigid-body | O 2 1.7 [1.1] 0.06 1.23 RB sampling 1F51 rigid-body | O 0 0.2 [0.5] 0.00 12.35 BB sampling 1E96 rigid-body | O 1 1.6 [1.1] 0.05 3.38 BB sampling 1KAC rigid-body | O 0 0.1 [0.5] 0.00 4.01 BB sampling 1I2M medium | O 1 1.5 [1.0] 0.03 2.68 BB sampling 1MLC rigid-body | A 0 0.1 [0.4] 0.00 4.31 BB sampling 1QFW rigid-body | AB 1 1.5 [1.1] 0.03 1.93 RB sampling 1S1Q rigid-body | O 0 0.1 [0.3] 0.00 4.37 BB sampling 1GLA rigid-body | O 2 1.5 [1.1] 0.05 2.98 BB sampling 1M10 medium | E 0 0.0 [0.0] 0.00 4.46 BB sampling 1AKJ rigid-body | O 1 1.2 [1.0] 0.02 1.48 BB sampling 1A2K rigid-body | O 0 0.0 [0.0] 0.00 5.20 BB sampling 1EZU rigid-body | E 1 1.2 [1.0] 0.02 2.82 RB sampling 1R8S difficult | O 0 0.0 [0.0] 0.00 5.21 BB sampling 1F34 rigid-body | E 1 1.2 [1.0] 0.02 4.00 RB sampling 1GP2 medium | O 0 0.0 [0.0] 0.00 5.23 BB sampling 1GRN medium | O 1 1.1 [1.0] 0.02 1.24 BB sampling 1IBR difficult | O 0 0.0 [0.0] 0.00 5.46 RB sampling 1NW9 medium | E 1 1.1 [1.0] 0.02 2.33 BB sampling 1BKD difficult | O 0 0.0 [0.0] 0.00 5.62 BB sampling 2H7V medium | O 1 1.1 [1.0] 0.02 3.65 BB sampling 2OT3 difficult | O 0 0.0 [0.0] 0.00 6.00 BB sampling 1GHQ rigid-body | O 1 1.0 [1.0] 0.01 2.69 BB sampling 1FQJ rigid-body | O 0 0.0 [0.0] 0.00 6.48 RB sampling 2NZ8 medium | O 1 1.0 [1.0] 0.02 3.91 BB sampling 1PXV difficult | E 0 0.0 [0.0] 0.00 9.49 BB sampling 1IB1 medium | O 1 1.0 [1.0] 0.01 3.95 discrimination 1H1V difficult | O 0 0.0 [0.0] 0.00 9.96 BB sampling 1K4C rigid-body | AB 1 1.0 [1.1] 0.02 2.15 BB sampling 1Y64 difficult | O 0 0.0 [0.0] 0.00 13.70 discrimination 1EWY rigid-body | E 1 1.0 [1.1] 0.02 3.01 BB sampling 1DQJ rigid-body | A 0 0.0 [0.2] 0.00 6.15 BB sampling 2PCC rigid-body | E 1 1.0 [0.9] 0.01 3.38 discrimination 1ACB medium | E 0 0.0 [0.1] 0.00 4.56 RB sampling 1KLU rigid-body | O 0 0.0 [0.1] 0.00 8.16 BB sampling Unsuccessful docking predictions are classified as cases for which the five lowest-energy decoys did not contain at least three near-native structures.

Publication Year: 2011


A minimalist model for ion partitioning and competition in a K+ channel selectivity filter.

(2011) J Gen Physiol 138

PubMed: 21875982 | PubMedCentral: PMC3171081 | DOI: 10.1085/jgp.201110694

1K4C ) comprising residues 73–81, followed by a sequence of uv calculations for drastically reduced filter models composed of mere carbonyl groups enclosing the binding sites S0–S4, S1... #x02013;S3, and S2 only.

Publication Year: 2011


Timothy mutation disrupts the link between activation and inactivation in Ca(V)1.2 protein.

(2011) J Biol Chem 286

PubMed: 21685391 | PubMedCentral: PMC3173108 | DOI: 10.1074/jbc.M111.255273

Channel Accessibilities of Amino Acids in the Bundle-crossing Region (Å 2 ) KcsA (PDB code 1k4c ) Thr-107 (5.9); Ala-108 ( 0.17 ); Ala-109 (14.19); Leu-110 (10.1).

Publication Year: 2011


Potassium-selective block of barium permeation through single KcsA channels.

(2011) J Gen Physiol 138

PubMed: 21911483 | PubMedCentral: PMC3182450 | DOI: 10.1085/jgp.201110684

1K4C ).

Publication Year: 2011


Thermodynamic coupling between activation and inactivation gating in potassium channels revealed by free energy molecular dynamics simulations.

(2011) J Gen Physiol 138

PubMed: 22124115 | PubMedCentral: PMC3226968 | DOI: 10.1085/jgp.201110670

1K4C ) and open (Protein Data Bank accession no.

1K4C ) after local alignment ( Zhou et al., 2001 ).

1K4C ) ( Zhou et al., 2001 ).

Adiabatic energy-minimized χ 1 , χ 2 maps of Phe103 in KcsA with the intracellular gate (A) closed (1K4C) and (B) open (Protein Data Bank accession no.

Publication Year: 2011


Probing the interaction of lipids with the non-annular binding sites of the potassium channel KcsA by magic-angle spinning NMR.

(2012) Biochim Biophys Acta 1818

PubMed: 21963409 | PubMedCentral: PMC3236287 | DOI: 10.1016/j.bbamem.2011.09.017

Subsequent studies have revealed the lipid present in the KcsA crystals to be phosphatidylglycerol which co-purifies with the KcsA [11] (pdb accession number 1K4C), suggesting that the phosphatidylgly... erol headgroup exhibits significant motion or disorder within the crystal, resulting in the absence of electron density.

Figure generated from pdb file 1K4C.

Publication Year: 2012


The crystal structure of a voltage-gated sodium channel.

(2011) Nature 475

PubMed: 21743477 | PubMedCentral: PMC3266868 | DOI: 10.1038/nature10238

Figure 2 NavAb pore module a, Pore-lining S6 helices of NavAb (yellow) and the closed MlotiK (3BEH), KcsA (1K4C) and NaK (2AHY) channels.

c, Superposition of NavAb and a K + -channel selectivity filter: NavAb Glu177 side-chains (purple) and backbone carbonyls (*); K + -channel (blue, 1K4C), site 3 and site 4 backbone carbonyls (ref.

Publication Year: 2011


Identification of putative potassium channel homologues in pathogenic protozoa.

(2012) PLoS One 7

PubMed: 22363819 | PubMedCentral: PMC3283738 | DOI: 10.1371/journal.pone.0032264

CNBD denotes a cyclic nucleotide monophosphate (cNMP) binding site [65] ; ( B ) A crystal structure of the KcsA pore domain is shown (PDB accession number 1K4C) [147] , with only the TMDs and pore loo... s of two subunits depicted for clarity.

Publication Year: 2012


Multiple binding sites for fatty acids on the potassium channel KcsA.

(2012) Biochemistry 51

PubMed: 22409348 | PubMedCentral: PMC3336937 | DOI: 10.1021/bi300153v

The coordinates were from Protein Data Bank entry 1K4C .

Publication Year: 2012


A molecular switch driving inactivation in the cardiac K+ channel HERG.

(2012) PLoS One 7

PubMed: 22848423 | PubMedCentral: PMC3404103 | DOI: 10.1371/journal.pone.0041023

We chose the highest-resolution structures of the KcsA SF backbone in their high-[K + ] (conductive, PDB ID 1K4C; [27] ) and low-[K + ] (collapsed, PDB ID 1K4D; [27] ) configurations a... comparison, and used the projection of the SF configurations on the difference vector between these extreme geometries as reaction coordinate.

To ensure a conductive conformation of the SF at the beginning of the simulations, the system was equilibrated for 1 ns with position restraints on the SF backbone atoms using the high-[K + ] crystal structure of KcsA as reference (PDB entry 1K4C [27] ) with a force constant of 1000 kJ mol −1 nm −2 .

The collective coordinate describing the transition between the high- and the low-[K + ] crystal structures of the KcsA SF was obtained by performing a principal component analysis of the SF backbone on the set of PDB entries 1K4C and 1K4D [27] .

For comparison, ( C ) displays the crystal structures of the collapsed (pdb: 1K4D) and ( D ) the conductive KcsA SF (pdb: 1K4C).

Publication Year: 2012


Structural changes during HCN channel gating defined by high affinity metal bridges.

(2012) J Gen Physiol 140

PubMed: 22930802 | PubMedCentral: PMC3434101 | DOI: 10.1085/jgp.201210838

1K4C ) and the cAMP-bound CNBD of spHCN (Protein Data Bank accession no.

Publication Year: 2012


Characterizing the fatty acid binding site in the cavity of potassium channel KcsA.

(2012) Biochemistry 51

PubMed: 22971149 | PubMedCentral: PMC3466778 | DOI: 10.1021/bi3009196

The coordinates were from Protein Data Bank entry 1K4C .

Publication Year: 2012


Ion conduction through the hERG potassium channel.

(2012) PLoS One 7

PubMed: 23133669 | PubMedCentral: PMC3487835 | DOI: 10.1371/journal.pone.0049017

Initial coordinates for the K + ions and water molecules in the filter were taken from the crystallographic structure of KcsA (PDB ID: 1K4C [8] ) upon superposition of the Cα atoms belonging t... the SF residues of the two channels.

All the dihedral reference values were taken by the crystallographic structure of KcsA (PDB ID: 1K4C [8] ).

Publication Year: 2012


Reliable B cell epitope predictions: impacts of method development and improved benchmarking.

(2012) PLoS Comput Biol 8

PubMed: 23300419 | PubMedCentral: PMC3531324 | DOI: 10.1371/journal.pcbi.1002829

The PDB files were further processed into 2 different files: 1) only containing the chain interacting with the antibody as original defined in the DiscoTope dataset and 2) PDB files containing additio... al structural information on the biological relevant unit (as described in the publication associated with the structure) if available (obtainable for PDB entry: 1XIW, 1TZH, 1CZ8, 1BJ1, 1K4D, 1K4C, 1KYO, 1EZV, 1NCA, 1NMC, 1A14, 1NCB, 1NCC, 1NCD, 1OTS, 1AR1, 1NFD, 2HMI, 1EO8, 1QFU).

Note, that the stated performances are for the PDB entry 1K4C and not the complete potassium homology group.

Publication Year: 2012


The open gate structure of the membrane-embedded KcsA potassium channel viewed from the cytoplasmic side.

(2013) Sci Rep 3

PubMed: 23323207 | PubMedCentral: PMC3545221 | DOI: 10.1038/srep01063

10827971 Figure 1 Crystal structure of the closed (residue 22–124) and open (residue 30–117) conformations of the KcsA channel (pdb code: 1K4C and 3F5W).

A vacant space was then created by removal of the DOPC and solution for filling the KcsA channel (PDB code: 1K4C) with F125 added to the C-terminal end (residues 22–125).

Starting from the closed structure (pdb code: 1K4C), the transmembrane region was made to move gradually to the templates of successively more widely open conformations (pdb code: 3F7Y, 3F7V, 3F5W; see the Methods section).

In both the open and closed states, the B-factors of the transmembrane helices obtained by the MD simulation were coincident with that of the closed (1K4C) structure, but smaller than the open (3F5W) structure.

Publication Year: 2013


Integrative Approach for Computationally Inferring Interactions between the Alpha and Beta Subunits of the Calcium-Activated Potassium Channel (BK): a Docking Study.

(2013) Bioinform Biol Insights 7

PubMed: 23492851 | PubMedCentral: PMC3588595 | DOI: 10.4137/BBI.S10077

29 , 30 The prediction was made by constructing a structure model by placing the backbone atoms of the target sequence at their aligned backbone positions of the selected structural templates (PDB IDs... 3naf, 1k4c and 1f6g).

Publication Year: 2013


Inter-?/? subunits coupling mediating pre-inactivation and augmented activation of BKCa(?2).

(2013) Sci Rep 3

PubMed: 23588888 | PubMedCentral: PMC3627188 | DOI: 10.1038/srep01666

During the modeling process, the S1-S6 domain was built from MthK (PDB:1LNQ) and KcsA (PDB:1K4C).

Publication Year: 2013


Atomic-level simulation of current-voltage relationships in single-file ion channels.

(2013) J Gen Physiol 141

PubMed: 23589581 | PubMedCentral: PMC3639580 | DOI: 10.1085/jgp.201210820

1K4C ; Zhou et al., 2001 ).

Publication Year: 2013


Probing the energy landscape of activation gating of the bacterial potassium channel KcsA.

(2013) PLoS Comput Biol 9

PubMed: 23658510 | PubMedCentral: PMC3642040 | DOI: 10.1371/journal.pcbi.1003058

Thus, the KcsA crystal structures (pdb identifier: 1k4c, closed; 3fb6, intermediate; 3f7v, open) were adjusted at the N- and C-termini so that all states started from residue 29 and ended at residue 1... 8, leading to channels with four times 89 amino acids.

Methods Simulation setup The closed (pdb identifier: 1k4c) [54] and open (pdb identifier: 3f7v) [12] crystal structures were used as starting conformations for the ED simulations.

Secondly, as expected [13] , KcsA crystal structures 1k4c, 3f7v, and 3fb6 occupy energy wells in our calculated energy profile ( Figure 4A ).

Publication Year: 2013


A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation.

(2013) J Gen Physiol 142

PubMed: 24043859 | PubMedCentral: PMC3787775 | DOI: 10.1085/jgp.201311049

1K4C ) are used to indicate the position of the sites within the filter and their occupancy by Ba 2+ ions (orange), K + ions (green), and Na + ions (purple).

1K4C ), which corresponds to a functional state with a closed intracellular gate.

1K4C ).

1K4C ) reported by Zhou et al. (2001) is embedded in a 70 Å × 70 Å bilayer comprised of 112 dipalmitoyl-phosphatidylcholine (POPC) lipids.

An initial grid of ion positions along the Z Ba axis was defined based on the locations of the ion binding sites in the 1K4C crystal structure.

Publication Year: 2013


Recovery from slow inactivation in K+ channels is controlled by water molecules.

(2013) Nature 501

PubMed: 23892782 | PubMedCentral: PMC3799803 | DOI: 10.1038/nature12395

A total of 114 MD simulations were carried out starting from different initial conditions with respect to the inactivating water molecules, for an aggregate total time of 29.5 μs of MD. FULL M... THODS Initial coordinates for the Molecular Dynamic (MD) simulations were taken from the crystal structures 1K4C and 1K4D.

Methods summary Initial coordinates for the Molecular Dynamic (MD) simulations were taken from the crystal structures 1K4C and 1K4D.

Publication Year: 2013


Molecular interactions involved in proton-dependent gating in KcsA potassium channels.

(2013) J Gen Physiol 142

PubMed: 24218397 | PubMedCentral: PMC3840921 | DOI: 10.1085/jgp.201311057

1K4C ; one subunit red) and an open mutant (Protein Data Bank accession no.

The data were phased using molecular replacement with Protein Data Bank accession number 1K4C as the starting model.

1K4C ).

1K4C ; residues are modeled as sticks with carbon yellow, nitrogen in blue, and oxygen in red) with a model of our R122A KcsA mutant structure (red sticks).

Publication Year: 2013


Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels.

(2013) J Chem Theory Comput 9

PubMed: 24353479 | PubMedCentral: PMC3864263 | DOI: 10.1021/ct4005933

Methods Producing Equilibrated Structures for Umbrella Sampling Crystallographic structures of KcsA 3 (PDB:1K4C) and Kvchim 4 (PDB: 2R9R) were obtained.

posA #sims k 12 k 3 kcsa-11 KcsA 1K4C( 3 ) yes yes GluH 577 40 or 80 20 kcsa-10 KcsA 1K4C( 3 ) yes no Ala 248 20 20 kcsa-00 KcsA 1K4C( 3 ) no no Ala 233 30 20 kvchim-10 Kvchim 2R9R( 4 ) yes no Val 480 80 or 20 20 kvchim-00 Kvchim 2R9R( 4 ) no no Val 233 80 or 30 20 kcsa-11a KcsA 1K4C( 3 ) yes yes GluH 196 40 20 kcsa-11b KcsA 1K4C( 3 ) yes yes GluH 381 80 20 kvchim-10a Kvchim 2R9R( 4 ) yes no Val 242 20 20 kvchim-10b Kvchim 2R9R( 4 ) yes no Val 237 80 or 20 20 a The kcsa-11 and kvchim-10 umbrella simulations can be further decomposed into two independent sets of simulations as shown, and hence, two 2D PMFs can be calculated from each (Figure 5 ).

Publication Year: 2013


Multiple mechanisms underlying rectification in retinal cyclic nucleotide-gated (CNGA1) channels.

(2013) Physiol Rep 1

PubMed: 24400150 | PubMedCentral: PMC3871463 | DOI: 10.1002/phy2.148

(C, D) Partial molecular structure of the KcsA channel (C) and NaK2CNG-E channel (D) as deposited in the Protein Data Bank (PDB entry code 1K4C and 3K0D, respectively) featuring the selectivity filter... and the P-helix in two adjacent subunits.

Publication Year: 2013


Non-equilibrium dynamics contribute to ion selectivity in the KcsA channel.

(2014) PLoS One 9

PubMed: 24465882 | PubMedCentral: PMC3895005 | DOI: 10.1371/journal.pone.0086079

The simulation system consisted of the tetrameric KcsA channel (PDB accession number 1K4C) embedded in a POPC lipid bilayer with associated water molecules.

The 1K4C crystal structure of KcsA was obtained at high K + concentration and is compatible with ion conduction [22] .

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4139162

20 Phases were obtained by molecular replacement using PHASER 21 with the structure of the Fab–KcsA complex [Protein Data Bank (PDB) entry 1K4C] as the search model.

14 The cocrystals diffracted X-rays to ∼2.4 Å Bragg spacings at the synchrotron, and the structures were determined by molecular replacement using the KcsA–Fab complex in potassium (PDB entry 1K4C) as the search model (Table 1 ).

Publication Year: 2014


NMDA receptor structures reveal subunit arrangement and pore architecture.

(2014) Nature 511

PubMed: 25008524 | PubMedCentral: PMC4263351 | DOI: 10.1038/nature13548

c , Superposition of the four M2 helices of the NMDA receptor onto the corresponding four M2 regions of the KcsA channel (PDB 1K4C; residues 61–75).

Publication Year: 2014


IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.

(2014) BMC Bioinformatics 15 Suppl 16

PubMed: 25521441 | PubMedCentral: PMC4290663 | DOI: 10.1186/1471-2105-15-S16-S9

Especially for the type AB (complexes of Antigen and the bound-Antibody), while ZDOCK was able to locate only one hit of 1 complex (i.e. [PDB:1K4C] shown in Additional file 1 ), the IFACEwat found 5 h... ts for 3 cases ([PDB:1K4C], [PDB:1IQD], and [PDB:1KXQ]) out of 7 cases and ranked the first hit as rank 1 for all these 3 cases.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4381907

Zhou Y , Morais-Cabral JH , Kaufman A , MacKinnon R , 2001 , Potassium Channel KcsA-Fab complex in high concentration of K+ , http://www.pdb.org/pdb/explore/explore.do?structureId=1K4C , Publicly avai... able at RCSB Protein Data Bank.

This is similar to the closed states of KcsA (pdb 1K4C [ Zhou et al., 2001 ]), NavAB (pdb 4EKW [ Payandeh et al., 2012 ]) and NavAP (pdb 4DXW [ Zhang et al., 2012 ]), where these values are 1.1, 1.2 and 0.9 Å respectively.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4411761

Figure 13 The KcsA potassium channels extracted in structures 1K4C, 1K4D and 1S5H.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4467903

It is a different picture for both of the transmembrane proteins (OmpF PDB: 4GCS( 48 ) and KcsA PDB: 1K4C( 47 )).

Table 1 Five Test Membrane Proteins a       number of type of membrane protein name PDB code atoms (AT) beads (CG) peripherial membrane proteins Phospholipase A2 1P2P( 44 ) 154 897 13 882   N-BAR 2RND( 45 ) 126 854 13 797 monotopic integral membrane proteins Cyclooxygenase 1 1PRH( 46 ) 194 871 17 632 polytopic integral membrane proteins KcsA 1K4C( 47 ) 125 081 11 376   OmpF 4GCS( 48 ) 121 237 11 495 a All were embedded in a simple lipid bilayer of 512 POPC molecules and were tested in both atomistic and coarse-grained representations.

Publication Year: 2015