Citations in PubMed

Primary Citation PubMed: 9309217 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 16

Citations in PubMed

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PDB ID Mentions in PubMed Central

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A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites.

(2007) BMC Bioinformatics 8 Suppl 4

PubMed: 17570152 | PubMedCentral: PMC1892088 | DOI: 10.1186/1471-2105-8-S4-S9

(A) Immunoglobulin 48g7 germline fab (PDB id: 1AJ7 and 2RCS); (B) Adenylate kinase (PDB id: 1AKE and 4AKE); (C) HIV-1 reverse transcriptase (PDB id: 1VRT and 1RTJ); (D) Maltodextrin binding protein (P... B id: 1ANF and 1OMP).

Publication Year: 2007


Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain.

(2008) BMC Struct Biol 8

PubMed: 18307765 | PubMedCentral: PMC2291057 | DOI: 10.1186/1472-6807-8-11

The structure was determined by molecular replacement with the program PHASER [ 43 ] using the known structure of MBP as phasing model (PDB accession number 1anf [ 44 ]).

Publication Year: 2008


Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis.

(2008) Acta Crystallogr D Biol Crystallogr 64

PubMed: 18094466 | PubMedCentral: PMC2394787 | DOI: 10.1107/S0907444907053516

Finally, the program was tested with real experimental data obtained from the PDB for the two forms of citrate synthase (PDB codes 5csc and 6csc ) and maltodextrin-binding protein (PDB codes 1anf and ... omp ) and the results were excellent using either five or ten modes (Delarue & Dumas, 2004 ▶ ).

Publication Year: 2008


Ligand-induced conformational changes in a thermophilic ribose-binding protein.

(2008) BMC Struct Biol 8

PubMed: 19019243 | PubMedCentral: PMC2630998 | DOI: 10.1186/1472-6807-8-50

PDB Entry Protein Apo Complex Reference Hinge Bending [ 25 ] Group I Escherichia coli leucine-binding protein 1USG 1USI Magnusson 2004[ 13 ] 14° Escherichia coli lactose repressor core 1TLF 1L... I Friedman 1995[ 42 ]; Lewis 1996[ 43 ] 15° Salmonella typhimurium autoinducer precursor-binding protein 1TM2 1TJY Miller 2004[ 28 ] 21° Neisseria gonorrhoeae ferric-binding protein 1R1N 1D9Y Zhu 2003[ 44 ]; McCree Unpublished 24° Thermotoga maritima ribose-binding protein 2FN9 2FN8 This Work 28° * Escherichia coli allose-binding protein 1GUD 1RPJ Chaudhuri 1999[ 45 ]; Magnusson 2002[ 7 ] 31° * Escherichia coli glucose-binding protein 2FW0 2FVY Borrok 2007[ 46 ] 31° Thermotoga maritima glucose/xylose-binding protein 3C6Q 2H3H Cuneo unpublished 38° Escherichia coli ribose-binding protein 1URP 2DRI Bjorkman 1998[ 8 ]; Bjorkman 1994[ 24 ] 43° * Group II Rhodobacter sphaeroides α-keto acid-binding protein 2HZK 2HZL Gonin 2007[ 47 ] 15° Escherichia coli nickel-binding protein 1UIU 1UIV Heddle 2003[ 48 ] 17° Homo sapiens glutamate receptor 1SYH 1N0T Frandsen 2005[ 49 ]; Hogner 2003[ 50 ] 18° Haemophilus influenzae ferric-binding protein 1D9V 1MRP Bruns 2001[ 51 ]; Bruns 1997[ 52 ] 20° Haemophilus influenzae sialic acid-binding protein 2CEY 2CEX Muller 2006[ 53 ] 25° Salmonella typhimurium oligopeptide-binding protein 1RKM 1RKM Sleigh 1997[ 54 ] 26° Escherichia coli phosphate-binding protein 1OIB 1QUK Yao 1996[ 55 ] 26° Mannheimia haemolytica ferric iron-Binding Protein 1SI1 1SI0 Shouldice 2004[ 56 ] 27° Vibrio harveyi autoinducer-binding protein 1ZHH 1JX6 Neiditch 2005[ 57 ]; Chen 2002[ 58 ] 27° Escherichia coli maltose-binding protein 1OMP 1ANF Sharff 1992[ 14 ]; Quiocho 1997[ 59 ] 36° Sphingomonas sp .

Publication Year: 2008


Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data.

(2010) Bioinform Biol Insights 4

PubMed: 20634984 | PubMedCentral: PMC2901630 | DOI: null

Protein Initial PDB Target PDB Number of residues Initial RMSD (Å) Final RMSD (Å) Without water With water Adenylate kinase 1AKE 4AKE 214 7.1 4.7 2.6 LAO blinding protein 2LAO 1LST 238... 4.7 \ 2.0 Maltodextrin blinding protein 1ANF 10MP 370 3.8 \ 2.0 Lactoferrin 1LFG 1LFH 691 6.4 \ \ Elongation factor 2 1NOV 1NOU 819 14.4 6.2 5.5 Note: \ indicates that no decrease in the RMSD was observed.

Publication Year: 2010


Mutations in maltose-binding protein that alter affinity and solubility properties.

(2010) Appl Microbiol Biotechnol 88

PubMed: 20535468 | PubMedCentral: PMC2940430 | DOI: 10.1007/s00253-010-2696-y

Secondary structural elements are indicated above the sequence, arrows for β-sheets and helices for α-helices, according to the PDB file 1ANF (Spurlino et al.

Structure from PDB file 1ANF rendered using PyMOL.

Publication Year: 2010


Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.

(2010) Open Biochem J 4

PubMed: 21293729 | PubMedCentral: PMC3032220 | DOI: 10.2174/1874091X01004010083

NMR X-ray PDB entry Chain Number of models PDB entry Chain Resolution (Å) 1 2JQX A 1 1D8C A 2.00 2 1EZO A 10 1ANF A 1.67 3 1AH2 A 18 1IAV A 1.80 4 1TR4 A 20 1UOH A 2.00 5 1BXL A 1 1MAZ A 2.20 ... 2GPQ A 10 1IPB A 2.00 7 1A23 A 1 1A2J A 2.00 8 1MM4 A 20 1THQ A 1.90 9 1GGR A 3 2F3G B 2.13 10 1CRP A 20 1GNP A 2.70 11 1OCA A 20 1W8L A 1.80 12 1NMV A 10 1PIN A 1.35 13 1AX3 A 16 1GPR A 1.90 14 1DF3 A 10 1JV4 A 1.75 15 1B6F A 23 1BV1 A 2.00 16 1EQ0 A 20 1DY3 A 2.00 17 1BVH A 15 1DG9 A 1.90 18 1RCH A 8 1RDD A 2.80 19 6I1B A 1 1I1B A 2.00 20 1BA9 A 36 1MFM A 1.02 21 1XPW A 20 1TVG A 1.60 22 1FXT A 1 1FZY B 1.90 23 1JOK A 1 1SNO A 1.70 24 1CFC A 25 1A29 A 2.74 25 1ORM A 20 1QJ8 A 1.90 26 1PFL A 20 1FIK A 2.30 27 1BLR A 22 1CBQ A 2.20 28 2P3M A 20 2VBS A 3.00 29 1JJJ A 20 1B56 A 2.05 30 1JBH A 20 1CRB A 2.10 31 1TBD A 1 2FUF A 1.45 32 1AEL A 20 1ICM A 1.50 33 1A63 A 10 1A62 A 1.55 34 1IY3 A 1 1IWT A 1.40 35 1CYL A 20 1HIK A 2.60 36 1CEY A 46 1CHN A 1.76 37 2JU3 A 10 1LFO A 2.30 38 1FR0 A 30 1A0B A 2.06 39 1GIO A 10 1AGI A 1.50 40 2PRF A 19 1PRQ A 2.50 41 1MVG A 10 1TVQ A 2.00 42 2AAS A 32 1AQP A 2.00 43 1FSP A 20 1NAT A 2.45 44 1PIR A 1 1P2P A 2.60 45 1IT4 A 1 1FAZ A 1.40 46 1KLV A 20 1GNU A 1.75 47 2JN8 A 20 2ES9 A 2.00 48 1SVQ A 20 1SVY A 1.75 49 1K19 A 20 1KX8 A 2.80 50 1BC4 A 15 1KM8 A 1.90 51 1BNR A 20 1YVS A 2.20 52 1A67 A 16 1CEW I 2.00 53 2NLN A 20 1OMD A 1.85 54 1F40 A 10 1FKB A 1.70 55 1MPH A 50 1BTN A 2.00 56 1N5H A 15 1PFP A 2.30 57 1IYY A 24 1BU4 A 1.90 58 2CZN A 38 2CWR A 1.70 59 1N7T A 20 2H3L B 1.00 60 2EVN A 20 2IL4 A 2.05 61 1GO0 A 10 1H7M A 1.96 62 1M42 A 1 2C9Q A 1.60 63 1IIY A 1 3EZM A 1.50 64 1JNJ A 20 1LDS A 1.80 65 1BEG A 18 1BEO A 2.20 66 1C15 A 16 1CY5 A 1.30 67 1BMW A 38 1WHO A 1.90 68 2JMV A 20 2QSK A 1.00 69 1AFH A 15 1FK0 A 1.80 70 3HSF A 30 2HTS A 1.83 71 1PQX A 10 2FFM A 2.51 72 1L8Y A 30 2HDZ A 2.00 73 2CKU A 15 2CG6 A 1.55 74 1A2S A 1 1CTJ A 1.10 75 1ACA A 20 1HB6 A 2.00 76 1GGR B 3 1POH A 2.00 77 1ACP A 2 1T8K A 1.10 78 1D3Z A 10 1AAR B 2.30 79 1RQS A 20 1CTF A 1.70 80 2AIT A 9 1HOE A 2.00 81 1FD8 A 1 1CC7 A 1.20 82 1K3G A 30 1C75 A 0.97 83 2ORC A 32 1ORC A 1.54 84 1HFG A 1 2FHT A 1.70 85 1ZUG A 20 2CRO A 2.35 86 1BQT A 6 1GZR B 2.0 87 3MEF A 16 1MJC A 2.00 88 2BTT A 20 1RUW A 1.80 89 1QQV A 1 1YU5 X 1.40 90 1LQH A 1 2ASC A 1.10 91 1IJC A 20 1F94 A 0.97 92 1AEY A 15 1SHG A 1.80 93 1ERA A 1 3EBX A 1.40 94 1ROF A 10 1VJW A 1.75 95 1JV8 A 23 1BPI A 1.09 96 1H0T B 40 1LP1 A 2.30 97 1KUN A 20 1KNT A 1.60 98 1GB1 A 60 1PGA A 2.07 99 1BFY A 20 1FHH A 1.50 100 1MBE A 1 1GUU A 1.60 101 1FDM 20 2C0W A 3.20 102 1CCM A 8 1CBN A 0.83 103 1PJF A 27 1QL1 A 3.10 104 1HEV A 6 1Q9B A 1.50 105 1ERC A 20 2ERL A 1.00 106 1KX6 A 20 1GCN A 3.00 107 1CIR B 20 1CIQ B 2.20 108 1V6R A 20 1EDN A 2.18 109 1XGA A 35 1NOT A 1.20 Table 2 Mean RMDS and RMDS 100 Values (Standard Deviations in Parenthesis) Calculated for the Superposed Equivalent X-Ray Protein Structure and NMR Models.

Publication Year: 2010


A genetically encoded, high-signal-to-noise maltose sensor.

(2011) Proteins 79

PubMed: 21989929 | PubMedCentral: PMC3265398 | DOI: 10.1002/prot.23118

To identify viable insertion sites, we used the crystal structures of the maltose-bound, closed form of MBP 39 (PDB 1ANF) and the ligand-free, open form of MBP 40 (PDB 1OMP) [ Fig. 1 (a)] to guide rat... onal design of MBP-cpGFP fusions that would result in maltose-dependent GFP fluorescence.

Publication Year: 2011


Determining biophysical protein stability in lysates by a fast proteolysis assay, FASTpp.

(2012) PLoS One 7

PubMed: 23056252 | PubMedCentral: PMC3463568 | DOI: 10.1371/journal.pone.0046147

BSA is α-helically folded (pdb identifier 1E7I), MBP has some β-sheets (pdb identifier 1JWY, 1ANF), PK contains more β-sheets (pdb identifier 1F3W), Sortase A mostly β-... heets (pdb identifier 1T2O) and folded Cytochrome C in presence of heme contains extended loops (pdb identifier 1AKK) [27] , [28] , [34] , [46] .

Publication Year: 2012


Analysis of conformational motions and residue fluctuations for Escherichia coli ribose-binding protein revealed with elastic network models.

(2013) Int J Mol Sci 14

PubMed: 23698778 | PubMedCentral: PMC3676853 | DOI: 10.3390/ijms140510552

Periplasmic binding proteins Pdb ID Correlation Reference Resolution (Å) Leucine-binding protein Apo 1USG 0.554 Magnusson 2004 [ 35 ] 1.53 Complex 1USI 0.64 1.8 Nickel-binding protein Apo 1UIU... 0.492 Heddle 2003 [ 36 ] 1.85 Complex 1UIV 0.531 1.95 Allose-binding protein Apo 1GUD 0.69 Chaudhuri 1999 [ 37 ] 1.71 Complex 1RPJ 0.594 Magnusson 2002 [ 8 ] 1.8 Glutamine-binding protein Apo 1GGG 0.488 Hsiao 1996 [ 38 ] 2.3 Complex 1ANF 0.581 Sun 1998 [ 39 ] 1.94 Maltose-binding protein Apo 1OMP 0.653 Sharff 1992 [ 40 ] 1.8 Complex 1ANF 0.594 Quiocho 1997 [ 41 ] 1.67 Ribose-binding protein Apo 1URP 0.583 Bjorkman 1998 [ 9 ] 2.3 Apo 1BA2 0.669 Bjorkman 1998 [ 9 ] 2.1 Complex 2DRI 0.772 Bjorkman 1994 [ 11 ] 1.6

Publication Year: 2013


SCEDS: protein fragments for molecular replacement in Phaser.

(2013) Acta Crystallogr D Biol Crystallogr 69

PubMed: 24189233 | PubMedCentral: PMC3817695 | DOI: 10.1107/S0907444913021811

  PDB code Modes NDOM Fragment 1 Fragment 2 Fragment 3 Fragment 4 Fragment 5 Excluded ( a ) Adenylate kinase, closed 2eck , chain B 7, 9 3 1–35, 68–124, 155–214 (CORE) ... 6–67 (NMP) 125–154 (LID) — — None ( b ) Adenylate kinase, open 4ake , chain A 7, 8 3 1–34, 68–117, 164–214 (CORE) 118–163 (LID) 35–67 (NMP) — — None ( c ) Calmodulin, closed 1ctr 9, 10 2 9–83 84–147 — — — 4–8 ( d ) Calmodulin, open 1cll 9, 10 2 12–72 88–147 — — — 1–11, 73–73, 81–87 ( e ) cAMP-dependent protein kinase 1atp , chain E 7, 8 2 15–35, 125–328 36–124, 222–350 — — — 329–332 ( f ) Citrate synthase 5csc , chain A 7, 8 2 1–82, 84–276, 385–433 277–291, 295–384 — — — None ( g ) Glutamine-binding protein 1ggg , chain A 8 2 5–82, 189–224 89–183 — — — 83–88, 184–188 ( h ) Maltodextrin-binding protein 1anf 7, 9 2 113–258, 319–370 8–112, 259–303 — — — 1–7 ( i ) Pyruvate phosphate dikinase 1kbl 11 4 566–828 6–243 244–380, 515–565, 829–873 381–514 — 2–5 ( j ) Pyruvate phosphate dikinase, triple mutant 2r82 7, 10 5 6–242 709–873 539–699 379–515 243–338 2–5, 340–370, 516–538, 700–708

( h ) Maltose-binding protein, PDB entry 1anf .

  Target Target Template Template   PDB code Conformer PDB code Conformer Training set  Alcohol dehydrogenase 6adh Closed 8adh Open  Alcohol dehydrogenase 8adh Open 6adh Closed  cAMP-dependent protein kinase 1atp Open 1ctp Closed  Citrate synthase 6csc Closed 5csc Open  Diptheria toxin 1mdt Closed 1ddt Open  Diptheria toxin 1ddt Open 1mdt Closed  Glutamine-binding protein 1wdn Closed 1ggg Open  Immunoglobulin 1hil , chain B Unbound 1him , chain M Bound  Lactoferrin 1flg Closed 1flh Open  Lactoferrin 1flh Open 1flg Closed  LAO binding protein 2lao Open 1lst Closed  Maltodextrin-binding protein 1anf Closed 1omp Open  Thymine synthase 2tsc Closed 3tms Open Test set  Adenylate kinase 1ake Open 2eck Closed  Adenylate kinase 2eck Closed 1ake Open  cAMP-dependent protein kinase 1ctp Open 1atp Closed  Calmodulin, closed 1ctr Closed 1cll Open  Calmodulin, open 1cll Open 1ctr Closed  Citrate synthase 6csc Closed 5csc Open  Glutamine-binding protein 1wdn Closed 1ggg Open  Maltodextrin-binding protein 1omp Open 1anf Closed  Pyruvate phosphate dikinase 1kbr Active 2t82 Inactive  Pyruvate phosphate dikinase 2t82 Inactive 1kbr Active Table 2 R values/ R free after ten cycles of REFMAC (Murshudov et al. , 2011 ▶ ) for structures of the whole template superimposed on the target (template) and after MR with the template divided into SCEDS fragments using the value of NDOM given The conformational change for calmodulin between the closed and open forms is too large to allow the whole template in one conformation to be superimposed on the target in the other conformation.

Publication Year: 2013


Four-body atomic potential for modeling protein-ligand binding affinity: application to enzyme-inhibitor binding energy prediction.

(2013) BMC Struct Biol 13 Suppl 1

PubMed: 24564918 | PubMedCentral: PMC3952120 | DOI: 10.1186/1472-6807-13-S1-S1

Our model 1ABE 6.52 5.25 -8.887610045 -10.3129 1ADB 8.40 8.01 -11.45029515 -23.3388 1ADD 6.74 5.36 -9.187498728 -13.1243 1AF2 3.10 4.90 -4.225704163 -10.0826 1ANF 5.46 6.03 -7.442691848 -9.59131 1CBX ... .35 5.74 -8.655877882 -11.6284 1DBM 9.44 6.65 -12.86795074 -14.9936 1DHF 7.40 5.27 -10.08716478 -13.1753 1GST 4.68 5.21 -6.379450155 -5.48917 1HPV 9.22 6.28 -12.56806206 -16.0903 X-Score: r = 0.67 Our model: r = 0.72 Experimental Δ G data for the complexes are derived from the experimental pk d values.

Publication Year: 2013


Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods.

(2013) BMC Struct Biol 13 Suppl 1

PubMed: 24564964 | PubMedCentral: PMC3953241 | DOI: 10.1186/1472-6807-13-S1-S2

Table 1 Proteins used in the overlap experiments Protein Residues PDB open PDB closed Che Y Protein 128 3chy 1chn LAO binding Protein 238 2lao 1laf Triglyceride Lipase 256 3tgl 4tgl Thymidulate Syntha... e 264 3tms 2tsc Maltodextrine Binding Protein 370 1omp 1anf Enolase 436 3enl 7enl Diphtheria Toxin 523 1ddt 1mdt For evaluating the capability of normal modes to predict directions of conformational transitions, we use the notion of overlap as proposed in related work [ 20 ].

Publication Year: 2013


Structural diversity of ABC transporters.

(2014) J Gen Physiol 143

PubMed: 24638992 | PubMedCentral: PMC3971661 | DOI: 10.1085/jgp.201411164

1ANF ), the cavity between two protein lobes connected by the hinge is accessible.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4410912

(C) The closed conformation of the MBP domain (PDB ID: 1ANF) with engineered disulfide bonds for RG13-ORN1 (P229C + P298C) and RG13-ORN2 (Q72C + P601C) shown in yellow spheres.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4520291

The assessment was performed on previously calculated fitted models resulting from flexible fitting by Flex-EM / RIBFIND (Pandurangan & Topf, 2012 ▸ ) of (i) the ligand-bound conformat... on of the glutamine-binding protein (PDB code 1wdn ; Sun et al. , 1998 ▸ ) in the density maps simulated from the ligand-free conformation (PDB code 1ggg ); (ii) the ligand-free maltodextrin binding protein (PDB code 1omp ; Sharff et al. , 1992 ▸ ) in the maps simulated from the ligand-bound conformation (PDB code 1anf ); and (iii) the ligand-bound d -ribose-binding protein (PDB code 2dri ; Björkman et al. , 1994 ▸ ) in the maps simulated from the ligand-free conformation (PDB code 1urp ).

At 20 Å resolution, using the Sobel filter with the NV score (NV-S) improves the discrimination between the top fits for both 1anf and 1urp .

Simulated benchmark: assessment of a local search ensemble and score performance   A total of 12 maps were simulated at 5, 10, 15 and 20 Å resolution from three known X-ray structures: the ligand-free glutamine-binding protein (PDB code 1ggg ; Hsiao et al. ,1996 ▸ ); the ligand-bound maltodextrin binding protein (PDB code 1anf ; Quiocho et al. , 1997 ▸ ); and the ligand-free d -ribose-binding protein (PDB code 1urp ; Björkman & Mowbray, 1998 ▸ ).

Publication Year: 2015