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PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies.

(2007) BMC Struct Biol 7

PubMed: 17509130 | PubMedCentral: PMC1888692 | DOI: 10.1186/1472-6807-7-31

The lowest correlation is for 1ctr with a correlation coefficient 0.63.

Protein ID (unbound-bound) Name of the protein Number of residues Ligand Rmsd between the structures (Å) 3chy - 1chn CheY 128 Mg 1.39 5dfr - 4dfr ^ Dihydrofolate Reductase 158 Methotrexate 0.80 1ctr - 1cll Calmodulin 138 Trifluoperazine 14.4 2lao - 1lst K-, R-, Orn-Binding Protein 238 Lys 4.70 3tms - 2tsc Thymidylate Synthase 264 UMP, CB3 0.80 1hka - 1rao HPPK (kinase) 158 AMP 3.13 1bbs - 1rne Renin 326 CGP, NAG 6.16 2a 6j - 2a6d * Antibody-Heavy chain 222 Dodecapeptide1 0.94 2a6j - 2a6i * Antibody-Heavy chain 222 Dodecapeptide2 1.10 2a6j - 2a6k * Antibody-Heavy chain 222 Dodecapeptide3 1.00 1oaq - 1oau Antibody-Heavy chain 121 DNP-Ser 0.62 1ocw - 1oaz Antibody-Heavy chain 121 Trx-Shear3 1.91 The first column lists the unbound and bound conformations PDB codes.

Table 2 Correlation coefficients between the real displacements and theoretical values Mode # 3chy 5dfr 1ctr 2lao 3tms 1hka 1bbs 1 0.60 0.66 0.47 0.37 0.10 0.72 0.60 2 0.73 0.42 0.14 0.84 0.70 0.85 0.40 3 0.68 0.43 0.63 0.23 0.05 0.87 0.71 (4) The first column gives the mode numbers, the first row lists the PDB IDs of the unbpund structures.

Publication Year: 2007


Using least median of squares for structural superposition of flexible proteins.

(2009) BMC Bioinformatics 10

PubMed: 19159484 | PubMedCentral: PMC2639377 | DOI: 10.1186/1471-2105-10-29

Table 1 Superposition results of protein systems with conformational changes using the LMS fit Protein system PDB1 PDB2 RMSD #Res 1 #Subset Core% 2 Time(s) ER α 3erd 3ert 4.9 244 203 83.2% 0.2... RAN 1byu 1rrp 14.4 200 141 70.5% 0.19 Myosin 1b7t 1dfk 13.0 720 403 56.0% 0.58 Calmodulin 1cll 1ctr 14.7 138 72 52.2% 0.09 Topo II 1bgw 1bjt 18.4 665 389 58.5% 0.55 Pneumolysin 2bk1 2bk2 21.8 435 139 32.0% 0.39 1 "#Res" is the number of atom pairs used for superposition by removing any inappropriate residues.

Figure 6 Superposition comparison for the Calmodulin structures: 1cll (light gray) and 1ctr (dark gray) .

Figure 10 Multiple level superposition for the Calmodulin structures: 1cll (light gray) and 1ctr (dark gray) .

We superimpose two conformational structures (1cll and 1ctr) of Calmodulin, where this hinge motion involves a long helix splitting into two helices and the angle between the axes of the two helical segments is about 100 degrees.

10 illustrates two level superposition for the Calmodulin structures: 1cll (light gray) and 1ctr (dark gray).

Publication Year: 2009


IDSS: deformation invariant signatures for molecular shape comparison.

(2009) BMC Bioinformatics 10

PubMed: 19463181 | PubMedCentral: PMC2694795 | DOI: 10.1186/1471-2105-10-157

(A) 1ctr .

Examples of simulated data The ability of inner distance to represent deformation invariant shape signatures of flexible molecules is first tested on some unrelated proteins (PDB code: 1ctr , 1b7t , 1irk and 2btv ).

Publication Year: 2009


Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.

(2011) BMC Struct Biol 11

PubMed: 21569443 | PubMedCentral: PMC3116463 | DOI: 10.1186/1472-6807-11-24

In order to validate the docking performance of DOCK6.0 we performed self-docking test with trifluoperazine on the X-ray PDB structure of the CaM-trifluoperazine complex (code 1CTR, 1:1 complex) follo... ing the same protocol.

Publication Year: 2011


SCEDS: protein fragments for molecular replacement in Phaser.

(2013) Acta Crystallogr D Biol Crystallogr 69

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

  Target Target Template Template   PDB code Conformer PDB code Conformer Training set  Alcohol dehydrogenase 6adh Closed 8adh Open  Alcohol dehydrogenase 8adh Open 6ad... 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.

  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) 36–67 (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

( c ) Calmodulin, PDB entry 1ctr .

Publication Year: 2013


Predicting drug-target interactions using probabilistic matrix factorization.

(2013) J Chem Inf Model 53

PubMed: 24289468 | PubMedCentral: PMC3871285 | DOI: 10.1021/ci400219z

48 We used as template the Protein DataBank (PDB) 49 structure of the cocrystal between calmodulin and trifluoperazine (PDB identifier 1CTR) 50 and examined the binding affinity of verapamil relative ... o that of trifluoperazine, using the module SMINA, 51 based on AutoDock VINA.

Publication Year: 2013


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4392415

The high-resolution structures of the protein calmodulin, a Ca 2+ -binding protein with a myriad of cellular functions dependent on its conformational state, were used to test the power of EOM 2.0 to ... iscriminate between open [PDB entry 1cll (Chattopadhyaya et al. , 1992 ▶ ), R g = 22.6 Å] and closed [PDB entry 1ctr (Cook et al .

Publication Year: 2015