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(-) Description

Title :  CRYSTAL STRUCTURE OF P450 2B4 F297A MUTANT IN COMPLEX WITH ANTI-PLATELET DRUG CLOPIDOGREL
 
Authors :  M. B. Shah, H. H. Jang, C. D. Stout, J. R. Halpert
Date :  10 Sep 12  (Deposition) - 16 Jan 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym./Biol. Unit :  A
Keywords :  P450, Cytochrome P450 2B4, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Shah, H. H. Jang, Q. Zhang, C. David Stout, J. R. Halpert
X-Ray Crystal Structure Of The Cytochrome P450 2B4 Active Site Mutant F297A In Complex With Clopidogrel: Insights Int Compensatory Rearrangements Of The Binding Pocket.
Arch. Biochem. Biophys. V. 530 64 2013
PubMed-ID: 23296089  |  Reference-DOI: 10.1016/J.ABB.2012.12.016

(-) Compounds

Molecule 1 - CYTOCHROME P450 2B4
    Chains: A
    EC Number: 1.14.14.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK
    Expression System Strain: TOPP3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CYP2B4, CYP2B6
    Mutation: YES
    Organism Common: EUROPEAN RABBIT,JAPANESE WHITE RABBIT,DOMESTIC RABBIT,RABBITS
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: CYPIIB4, CYTOCHROME P450 ISOZYME 2, CYTOCHROME P450 LM2, CYTOCHROME P450 TYPE B0, CYTOCHROME P450 TYPE B1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1CGE1Ligand/IonCLOPIDOGREL
2CM53Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:98 , ILE A:114 , TRP A:121 , ARG A:125 , ILE A:179 , ALA A:298 , GLY A:299 , THR A:303 , ILE A:363 , VAL A:367 , HIS A:369 , LEU A:392 , PRO A:428 , PHE A:429 , SER A:430 , ARG A:434 , CYS A:436 , GLY A:438 , ALA A:442 , CGE A:505BINDING SITE FOR RESIDUE HEM A 501
2AC2SOFTWAREGLU A:250 , GLU A:322BINDING SITE FOR RESIDUE CM5 A 502
3AC3SOFTWARELEU A:43 , MET A:46 , ASP A:47BINDING SITE FOR RESIDUE CM5 A 503
4AC4SOFTWARELYS A:186 , PHE A:188 , PHE A:195 , LEU A:198 , PHE A:244 , PHE A:296BINDING SITE FOR RESIDUE CM5 A 504
5AC5SOFTWAREILE A:101 , ILE A:114 , ILE A:209 , ALA A:297 , ALA A:298 , VAL A:367 , VAL A:477 , HEM A:501BINDING SITE FOR RESIDUE CGE A 505
6AC6SOFTWARETHR A:404 , PRO A:405 , ASN A:406 , THR A:407BINDING SITE FOR RESIDUE SO4 A 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H1N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H1N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H1N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H1N)

(-) Exons   (0, 0)

(no "Exon" information available for 4H1N)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh..hhhhhee.....hhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeee...hhhhh...............eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h1n A  29 KLPPGPSPLPVLGNLLQMDRKGLLRSFLRLREKYGDVFTVYLGSRPVVVLCGTDAIREALVDQAEAFSGRGKIAVVDPIFQGYGVIFANGERWRALRRFSLATMRDGKRSVEERIQEEARCLVEELRKSKGALLDNTLLFHSITSNIICSIVFGKRFDYKDPVFLRLLDLFFQSFSLISSFSSQVFELFSGFLKYFPGTHRQIYRNLQEINTFIGQSVEKHRATLDPSNPRDFIDVYLLRMEKDKSDPSSEFHHQNLILTVLSLFAAGTETTSTTLRYGFLLMLKYPHVTERVQKEIEQVIGSHRPPALDDRAKMPYTDAVIHEIQRLGDLIPFGVPHTVTKDTQFRGYVIPKNTEVFPVLSSALHDPRYFETPNTFNPGHFLDANGALKRNEGFMPFSLGKRICLGEGIARTELFLFFTTILQNFSIASPVPPEDIDLTPSGVGNVPPSYQIRFLARH 492
                                    38        48        58        68        78        88        98       108       118       128     ||141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471||     483         
                                                                                                                                   134|                                                                                                                                                                                                                                                                                                                                           472|                 
                                                                                                                                    138                                                                                                                                                                                                                                                                                                                                            475
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4H1N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H1N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H1N)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  4h1n
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  CP2B4_RABIT | P00178
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CP2B4_RABIT | P00178: 1po5 1suo 2bdm 2q6n 3g5n 3g93 3kw4 3me6 3mvr 3r1a 3r1b 3tk3 3tmz 3uas 4jlt 4mgj 5em4 5iut 5iuz

(-) Related Entries Specified in the PDB File

1po5 THE SAME PROTEIN WITHOUT H226Y AND F297A MUTATION IN A LIGAND FREE OPEN CONFORMATION
1suo THE SAME PROTEIN WITHOUT F297A MUTATION IN COMPLEX WITH 4- (4-CHLOROPHENYL)IMIDAZOLE
2bdm THE SAME PROTEIN WITHOUT F297A MUTATION IN COMPLEX WITH BIFONAZOLE
2q6n THE SAME PROTEIN WITHOUT F297A MUTATION IN COMPLEX WITH 1- (4-CHLOROPHENYL)IMIDAZOLE
3g5n THE SAME PROTEIN WITHOUT F297A MUTATION IN COMPLEX WITH 1- BIPHENYL-4-METHYL-1H-IMIDAZOLE (TRIPLE LIGAND OCCUPANCY)
3g93 THE SAME PROTEIN WITHOUT F297A MUTATION IN COMPLEX WITH 1- BIPHENYL-4-METHYL-1H-IMIDAZOLE (SINGLE LIGAND OCCUPANCY)
3kw4 THE SAME PROTEIN WITHOUT F297A MUTATION IN COMPLEX WITH TICLOPIDINE
3me6 THE SAME PROTEIN WITHOUT F297A MUTATION IN COMPLEX WITH CLOPIDOGREL
3mvr THE SAME PROTEIN WITHOUT F297A MUTATION IN A LIGAND FREE CLOSED CONFORMATION
3r1a THE SAME PROTEIN WITHOUT F297A MUTATION IN COMPLEX WITH TERT-BUTYLPHENYLACETYLENE (CLOSED CONFORMATION)
3r1b THE SAME PROTEIN WITHOUT F297A MUTATION IN COMPLEX WITH TERT-BUTYLPHENYLACETYLENE (OPEN CONFORMATION)