Citations in PubMed

Primary Citation PubMed: 14563924 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

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 Conformation 1 a Conformation 2 a PDB id Δ G calc D τ PDB id Δ G calc D τ Signal peptidase A.1 1kn9 -4.5 4.5 83 1t7d -5.9 3.7 66 Cytochrome P450 2b4 A.... 1po5 -6.9 9.7 39 2bdm -18.2 10.5 45 Cytochrome P450 2c5 A.1 1nr6 -11.6 12.5 54 1dt6 -8.4 7.5 17 Cytochrome P450 2c9 A.1 1og5 -13.6 7.5 74 1r9o -10.7 7.5 57 Cytochrome P450 3a4 A.1 1tqn -20.7 10.2 61 1w0f -15.2 6.2 68 Bile-salt activated lipase C.1 1aql -9.7 6.0 80 1akn -6.6 5.7 67 Triacylglycerol lipase C.1 1tib -3.3 1.9 42 1dt5 -4.8 2.9 84 Lipase/colipase complex C.1 1lpa -22.1 8.7 89 1lpb -26.2 10.3 87 Ganglioside GM2 activator C.2 1tjj -9.3 4.6 55 1pub -7.8 5.2 44 Phosducin/βγ complex C.3 1a0r -3.7 2.7 45 2trc -2.9 4.4 64 Tubby protein C.4 1c8z -4.2 6.2 87 1i7e -3.6 2.6 78 a All structures were solved by X-ray crystallography.

Publication Year: 2007


TransCent: computational enzyme design by transferring active sites and considering constraints relevant for catalysis.

(2009) BMC Bioinformatics 10

PubMed: 19208235 | PubMedCentral: PMC2667513 | DOI: 10.1186/1471-2105-10-54

The last line gives the native sequence as deduced from pdb-entry 1po5 .

In the left panel, the active site of cytochrome P450 ( 1po5 ) is plotted; in the right panel, the active site of the best model generated by TransCent is shown.

Oxidoreductase cytochrome P450 2B4 (pdb code 1po5 [ 35 ]) is – according to the SCOP classification [ 36 ] – an all-alpha protein.

Publication Year: 2009


Comparative modeling and molecular docking of orphan human CYP4V2 protein with fatty acid substrates: Insights into substrate specificity.

(2011) Bioinformation 7

PubMed: 22355237 | PubMedCentral: PMC3280491 | DOI: null

Supplementary material Data 1 Citation: Kumar, Bioinformation 7(7): 360 365 (2011) References 1 RL Strausberg Proc Natl Acad Sci USA 2002 99 16899 12477932 2 FP Guengerich Biochem Biophys Res Commun 2... 05 338 465 16126164 3 A Li Am J Hum Genet 2004 74 817 15042513 4 Y Wada Am J Ophthalmol 2005 139 894 15860296 5 TY Lai Invest Ophthalmol Vis Sci 2007 48 5212 17962476 6 DJ Wilson Arch Ophthalmol 1989 197 213 2783846 7 M Nakano Drug Metab Dispos 2009 37 2119 19661213 8 SF Altschul J Mol Biol 1990 215 403 2231712 9 A Sali Proteins 1995 23 318 8710825 10 E Krieger Proteins 2009 77 114 19768677 11 F Glaser Bioinformatics 2003 19 163 12499312 12 NM O'Boyle J Cheminform 2011 3 33 21982300 13 CA Lipinski Adv Drug Del Rev 2001 46 3 11259830 14 Z Bikadi E Hazai J Cheminform 2009 11 1 20150996 15 GM Morris J Comput Chem 2009 30 2785 19399780 16 DF Lewis Mutat Res 1998 410 245 9630657 17 P Gajendrarao J Mol Graph Model 2010 28 524 20079672 18 AL Morris Proteins 1992 12 345 1579569 19 M Wiederstein MJ Sippl Nucleic Acids Res 2007 35 W407 17517781 20 T Castrignanò Nucleic Acids Res 2006 34 D306 16381873 Figure 1 Multiple sequence alignment of target (CYP4V2: Q6ZWL3) and six templates (3EBS, 1PO5, 1NR6, 3E4E, 3CZH and 1TQN) using ClustalW program.

Publication Year: 2011


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