Citations in PubMed

Primary Citation PubMed: 12899620 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


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).

Glu310 coincides with an aspartic acid in the CYP2 family which from visual inspection of the crystal structures of CYP2C5 (pdb-code 1NR6) and CYP2C9 (pdb-code 1OG5) seems to play a specific stabilising role in the active site structure; it is expected that Glu310 has the same stabilising role.

Table 2 Validation results for the lowest energy models of CYP11B1 and CYP11B2 and the crystal structures which were used for the template, part I Ramachandran Plot (core regions) (%) Ramachandran Plot (favourable regions) (%) Errat2 (quality factor, %) a Verify 3D (total score) b Template ( PDB, resolution ) CYP101 (2CPP, 1.63 Å) 92.1 100.0 96.0 197 CYP2C5 (1NR6, 2.10 Å) 87.8 99.2 93.6 195 Model hCYP11B1 78.8 94.7 84.1 126 hCYP11B2 78.7 94.7 87.5 125 hCYP11B2-TripMut 80.6 96.5 81.1 117 rCYP11B1 79.7 96.5 80.2 113 rCYP11B2 82.4 96.5 80.1 114 a   Outliers are positioned in the loop regions before alpha-helix F where the two template structures connect and at the end of alpha-helix D where a large insertion was introduced b   Additional outliers are positioned at the end of alpha-helix G For both hCYP11B1 and hCYP11B2 around 95% of the residues are positioned in the favoured and core regions of the Ramachandran Plot, indicating that for hybrid models, the structures are of acceptable quality.

Publication Year: 2007


Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila.

(2009) BMC Genomics 10

PubMed: 19409101 | PubMedCentral: PMC2691746 | DOI: 10.1186/1471-2164-10-208

Previously reported P450 protein crystal structure data were downloaded from the RCSB (Brookhaven protein data bank) website , including P450cam (CYP101), P450BM3 (CYP102), P450terp (CYP108) and P450e... yF (CYP107A1) from bacteria, P450nor (CYP55A1) from fungi, CYP2C5, CYP2C8 and CYP3A4 from mammals, corresponding to PDB codes 1UTU, 1ZO4, 1CPT, 1EUP, 1EHE, 1NR6, 1PQ2 and 1TQN, respectively.

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


Study on incompatibility of traditional chinese medicine: evidence from formula network, chemical space, and metabolism room.

(2013) Evid Based Complement Alternat Med 2013

PubMed: 24369478 | PubMedCentral: PMC3858019 | DOI: 10.1155/2013/352145

The crystal structures of these enzymes were collected from PDB, with the names and their PDB code as follows: CYP 1A1 (PDB code: 4I8V), CYP 1A2 (PDB code: 2HI4), CYP 1B1 (PDB code: 3PM0), CYP 2A6 (PD... code: 1Z10), CYP 2A13 (PDB code: 2PB5), CYP 2B4 (PDB code: 3TMZ), CYP 2B6 (PDB code: 3UA5), CYP 2C5 (PDB code: 1NR6), CYP 2C8 (PDB code: 2VN0), CYP 2C9 (PDB code: 1R9O), CYP 2C18 (PDB code: 2H6P), CYP 2C19 (PDB code: 4GQS), CYP 2D6 (PDB code: 3TDA), CYP 2E1 (PDB code: 3T3Z), and CYP 3A4 (PDB code: 3NXU).

Publication Year: 2013