Citations in PubMed

Primary Citation PubMed: 15100217 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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The role of hydrophobic interactions in positioning of peripheral proteins in membranes.

(2007) BMC Struct Biol 7

PubMed: 17603894 | PubMedCentral: PMC1934363 | DOI: 10.1186/1472-6807-7-44

Protein Category "Closed" state "Open"/lipid-bound state PDB id Δ G calc D τ PDB id Δ G calc D τ Cytochrome P450 2b4 A.1 1suo -13.0 4.7 54 2bdm -18.2 10.5 45 Fungal lip... se 1 C.1 1trh -7.8 3.0 80 1lpp -30.6 9.1 84 Triacylglycerol lipase Rhizomucor miehei C.1 3tgl -4.1 4.5 28 4tgl -14.0 4.9 55 Triacylglycerol lipase Humicola lanuginose C.1 1tib -3.3 1.9 42 1ein -13.5 9.5 71 Gastric lipase a C.1 1hlg -5.0 3.4 6 1k8q -10.8 6.3 80 α-Toxin (Phospholipase C) C.1 1gyg -4.2 5.5 60 1ca1 -4.5 2.2 88 Alpha-tocopherol transfer protein C.2 1r5l -10.6 4.0 81 1oiz -20.7 8.4 63 Glycolipid transfer protein C.2 1swx -4.9 3.4 86 1sx6 -7.9 3.9 87 Ganglioside GM2 activator C.2 2ag4 -5.1 4.2 47 1tjj -9.3 4.6 55 Synaptotagmin C2A domain of b C.4 1rsy -3.3 2.1 26 1byn c -4.4 3.7 36 Mersacidin d C.7 1mqx c -2.3 2.4 77 1mqy c -9.5 11.5 56 a The open and closed forms of gastric lipase are taken from closely related species.

Publication Year: 2007


Construction of 3D models of the CYP11B family as a tool to predict ligand binding characteristics.

(2007) J Comput Aided Mol Des 21

PubMed: 17646925 | PubMedCentral: PMC2039848 | DOI: 10.1007/s10822-007-9128-9

Species information: Pseudomonas-Putida 2CPP, Bacillus Megaterium 1BU7, Saccharopolyspora-Erythreaea 1JIN, Pseudomonas -SP 1CPT, Archaeon Sulfolobus Solfataricus 1F4U, Fusarium-Oxysporum 1ROM, Mycobac... erium Tuberculosis 1EA1, Oryctolagus Cuniculus 1SUO and 1NR6, Homo Sapiens 1PQ2, 1OG2, 1W0E and 2F9Q Because of the low sequence identity of the CYP11B family, we have chosen to create a hybrid template for hCYP11B2 using MOE-Homology [ 42 ], constructed from the crystal structures of CYP101 (pdb code: 2CPP) and CYP2C5 (pdb code: 1NR6).

Publication Year: 2007


Prediction and analysis of the modular structure of cytochrome P450 monooxygenases.

(2010) BMC Struct Biol 10

PubMed: 20950472 | PubMedCentral: PMC3224734 | DOI: 10.1186/1472-6807-10-34

CYP PDB entry Resolution [Å] Ligand Organism Class II CYPs (CPR-type) 1A2 2HI4 1.95 + Homo sapiens 2A6 1Z10 1.90 + Homo sapiens 2A13 2P85 2.35 + Homo sapiens 2B4 1SUO 1.90 + Oryctolagus cunicu... us 2C5 1N6B 2.30 + Oryctolagus cuniculus 2C8 1PQ2 2.70 + Homo sapiens 2C9 1OG2 2.60 + Homo sapiens 2D6 2F9Q 3.00 - Homo sapiens 2R1 2OJD 2.80 + Homo sapiens 3A4 1TQN 2.05 - Homo sapiens 102A1 1BU7 1.65 - Bacillus megaterium (P450 BM-3) 175A1 1N97 1.80 - Thermus thermophilus Class I CYPs 51B1 1E9X 2.10 + Mycobacterium tuberculosis 101D 2CPP 1.63 + Pseudomonas putida (P450cam) 107A1 1OXA 2.10 + Saccharopolyspora erythrea 107L1 2BVJ 2.10 - Streptomyces venezuelae 108A 1CPT 2.30 - Pseudomonas sp .

Table 2 Positions which correspond to F87 in P450 BM-3 and predicted position, and prediction of positions in new structures CYP PDB-Code Position in crystal structure Predicted position 8A 2IAG - - 51B1 1E9X - V88 55A2 1CL6 V87 V87 101D 2CPP T101 I99 107A1 1OXA G91 G91 107L1 2BVJ L93 L93 108A 1CPT T103 T103 119 1IO7 L69 L69 152A1 1IZO Q85 Q85 154A1 1ODO F88 F88 154C1 1GWI L93 L93 158A1 2DKK A97 S95 158A2 1S1F G94 G94 165B3 1LFK M89 N87 165C4 1UED S98 S98 167A1 1Q5D F96 G94 175A1 1N97 L80 L80 176A1 1T2B A91 M89 199A2 2FR7 L100 L100 245A1 2Z3T V99 V99 1A2 2HI4 T124 S126 2A6 1Z10 V117 V117 2A13 2P85 A117 A117 2B4 1SUO I114 I114 2C5 1N6B A113 A113 2C8 1PQ2 I113 I113 2C9 1OG2 V113 V113 2D6 2F9Q F120 F120 2R1 2OJD L125 L125 3A4 1TQN S119 S119 102A1 1BU7 (reference) F87 F87 2E1 3E4E I94 I94 3A43 2V0M S119 S119 7A1 2DAX - D98 19A1 3EQM F134 F134 46A1 2Q9F V126 S127 74A1 2RCH S128 L127 105A1 2ZBX I96 I96 105K1 2Z36 L96 L96 120A1 2VE3 A94 A94 231A2 2RFB I48 I48 248A 3BUJ L80 L80 To validate our structure-based method to assign SCRs in a one-leave-out cross-validation, the position which corresponds to F87 in CYP102A1 was predicted for each sequence of each structure.

Publication Year: 2010


Rapid and accurate prediction and scoring of water molecules in protein binding sites.

(2012) PLoS One 7

PubMed: 22396746 | PubMedCentral: PMC3291545 | DOI: 10.1371/journal.pone.0032036

Protein PDB code Resolution (Å) Ligand BRD4 2OSS 1.35 None BRD4 3MXF 1.6 JQ1 Trypsin 1SOQ 1.02 None Trypsin 1BTY 1.5 Benzamidine HSP 90 a 1AH6 1.8 None HSP 90 1AM1 2 ADP Penicillopepsin a 3APP... 1.8 None Penicillopepsin 1BXQ 1.41 PPi3 Cytochrome P450 2B4 1PO5 1.6 None Cytochrome P450 2B4 1SUO 1.9 4-(4-chlorophenyl) imidazole PIM1 kinase a 1YWV 2 None PIM1 kinase 1XWS 1.8 BI1 Purine nucleoside phosphorylase 1V48 2.2 DFPP-G GluA2 ligand binding core 1FTM 1.7 AMPA HIV-1 protease 1KZK 1.09 JE-2147 a Structures that were selected for molecular dynamics simulations.

Publication Year: 2012


Perturbation centrality and turbine: a novel centrality measure obtained using a versatile network dynamics tool.

(2013) PLoS One 8

PubMed: 24205090 | PubMedCentral: PMC3804472 | DOI: 10.1371/journal.pone.0078059

Generating protein structure networks from structure information Protein structure networks from the substrate-free and substrate-bound form of methionyl-tRNA synthetase enzyme (Met tRNA synthase [43]... ), as well as the substrate-free (1PO5, [55] ) and imidazole-bound (1SUO, [56] ) form of rabbit cytochrome P450 2B4 were built with the RINerator software [5] , using the PDB files received from the authors of [43] in the case of MetRS, and using the published 1PO5 and 1SUO structures from the Protein Data Bank.

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4131899

Its overall structure is a closed conformation similar to that of the 4-CPI-bound wild type protein [Protein Data Bank (PDB) entry 1SUO].

Figure 5 Structure of the β-bulge and β-turn of CYP2B4 (PDB entry 1SUO).

Table 5 Amide Hydrogen and Thiolate Bond Distances and N–H···S Angles for the Three Heme Pocket Residues C-Terminal to Cys (Cys-X1-Gly-X3)       bond distance a (H···S) (Å) angle (N–H···S) (deg) P450 (PDB entry) P450 class resolution (Å) X1 G X3 X1 G X3 Fe 3+ cam (2CPP) I 1.63 3.7 2.5 3.2 73 129 91 11A1 (3N9Y) I 2.1 3.6 2.6 3.1 73 123 89 2B4 (1SUO) II 1.6 3.7 2.5 3.4 77 137 88 2B4 F429H/4-CPI II 2.4 3.7 2.6 3.4 76 129 82 1A2 (2HI4) II 1.95 3.5 2.3 3.2 76 147 89 102 μ B 3 (2J1M) II 1.7 3.8 2.5 3.3 73 133 92 3A4 (3UA1) II 2.15 3.9 2.8 3.4 75 128 83 176A1cin (4FMX) II 1.55 3.6 2.6 3.4 77 136 87 152B1 SPα (3AWM) III 1.65 Pro 2.3 3.8 Pro 146 93 74A AOS (2RCH) III 1.85 3.7 2.5 3.6 75 140 85 8A1 (2B99) III 2.50 Pro 2.6 3.3 Pro 133 102 55NOR (1JFB) IV 1.0 3.6 2.6 3.5 81 140 87 mean ± standard deviation     3.7 ± 0.1 2.5 ± 0.1 3.3 ± 0.2 74 ± 3 137 ± 8 90 ± 6 a Hydrogen atoms were calculated in COOT.

Publication Year: 2014


Insights into the role of substrates on the interaction between cytochrome b5 and cytochrome P450 2B4 by NMR.

(2015) Sci Rep 5

PubMed: 25687717 | PubMedCentral: PMC4330534 | DOI: 10.1038/srep08392

Figure 5 Electrostatic potential surfaces of the proximal sides of cyt b 5 (left) and CYP2B4 (right), showing the negatively charged convex surface of cyt b 5 (PDB code: 2M33) 24 and the positively ch... rged concave surface of CYP2B4 (PDB code: 1SUO 34 ).

Publication Year: 2015