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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYTOCHROME P450 3A4
 
Authors :  P. A. Williams, J. Cosme, D. M. Vinkovic, A. Ward, H. C. Angove, P. J. Day, C. Vonrhein, I. J. Tickle, H. Jhoti
Date :  03 Jun 04  (Deposition) - 22 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Nifedipine Oxidase, Cytochrome P450, Electron Transport, Monooxygenase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. A. Williams, J. Cosme, D. M. Vinkovic, A. Ward, H. C. Angove, P. J. Day, C. Vonrhein, I. J. Tickle, H. Jhoti
Crystal Structures Of Human Cytochrome P450 3A4 Bound To Metyrapone And Progesterone
Science V. 305 683 2004
PubMed-ID: 15256616  |  Reference-DOI: 10.1126/SCIENCE.1099736

(-) Compounds

Molecule 1 - CYTOCHROME P450 3A4
    ChainsA
    EC Number1.14.13.67, 1.14.14.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainXL1 BLUE
    Expression System Taxid562
    Expression System VectorPCWORI(+)
    FragmentSOLUBLE DOMAIN, RESIDUES 24-502
    OrganLIVER
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymQUININE 3-MONOOXYGENASE, CYPIIIA4, NIFEDIPINE OXIDASE, NF-25, P450-PCN1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MYT1Ligand/IonMETYRAPONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:105 , ILE A:118 , TRP A:126 , ARG A:130 , PHE A:137 , PHE A:302 , ALA A:305 , THR A:309 , ARG A:375 , PRO A:434 , PHE A:435 , GLY A:436 , SER A:437 , ARG A:440 , ASN A:441 , CYS A:442 , ILE A:443 , ALA A:448 , MYT A:1499BINDING SITE FOR RESIDUE HEM A1501
2AC2SOFTWARESER A:119 , ALA A:305 , THR A:309 , ALA A:370 , HEM A:1501BINDING SITE FOR RESIDUE MYT A1499

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W0G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W0G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (20, 20)

Asymmetric/Biological Unit (20, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_011598G56DCP3A4_HUMANPolymorphism56324128AG56D
02UniProtVAR_037547K96ECP3A4_HUMANPolymorphism3091339AK96E
03UniProtVAR_011599I118VCP3A4_HUMANPolymorphism55951658AI118V
04UniProtVAR_011600R130QCP3A4_HUMANPolymorphism72552799AR130Q
05UniProtVAR_011601R162QCP3A4_HUMANPolymorphism4986907AR162Q
06UniProtVAR_011602V170ICP3A4_HUMANPolymorphism72552798AV170I
07UniProtVAR_011603D174HCP3A4_HUMANPolymorphism4986908AD174H
08UniProtVAR_011604T185SCP3A4_HUMANPolymorphism12721627AT185S
09UniProtVAR_014322F189SCP3A4_HUMANPolymorphism4987161AF189S
10UniProtVAR_011605P218RCP3A4_HUMANPolymorphism55901263AP218R
11UniProtVAR_008363S222PCP3A4_HUMANPolymorphism55785340AS222P
12UniProtVAR_037548S252ACP3A4_HUMANPolymorphism3208363AS252A
13UniProtVAR_014323L293PCP3A4_HUMANPolymorphism28371759AL293P
14UniProtVAR_037549T349NCP3A4_HUMANPolymorphism10250778AT349N
15UniProtVAR_011606T363MCP3A4_HUMANPolymorphism67784355AT363M
16UniProtVAR_011607L373FCP3A4_HUMANPolymorphism12721629AL373F
17UniProtVAR_011608P416LCP3A4_HUMANPolymorphism4986909AP416L
18UniProtVAR_037550I431TCP3A4_HUMANPolymorphism1041988AI431T
19UniProtVAR_008364M445TCP3A4_HUMANPolymorphism4986910AM445T
20UniProtVAR_014324P467SCP3A4_HUMANPolymorphism4986913AP467S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP3A4_HUMAN435-444  1A:435-444

(-) Exons   (12, 12)

Asymmetric/Biological Unit (12, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003364111aENSE00001957287chr7:99381888-99381634255CP3A4_HUMAN1-24240--
1.2bENST000003364112bENSE00001696932chr7:99377708-9937761594CP3A4_HUMAN24-55321A:25-5531
1.3bENST000003364113bENSE00001786394chr7:99375703-9937565153CP3A4_HUMAN56-73181A:56-7318
1.4ENST000003364114ENSE00001055096chr7:99370312-99370213100CP3A4_HUMAN73-106341A:73-10634
1.5bENST000003364115bENSE00001630478chr7:99367858-99367745114CP3A4_HUMAN107-144381A:107-14438
1.6aENST000003364116aENSE00001766439chr7:99367479-9936739189CP3A4_HUMAN145-174301A:145-17430
1.7ENST000003364117ENSE00001717945chr7:99366125-99365977149CP3A4_HUMAN174-224511A:174-22451
1.8ENST000003364118ENSE00001055106chr7:99364881-99364754128CP3A4_HUMAN224-266431A:224-26239
1.9ENST000003364119ENSE00001784871chr7:99364066-9936400067CP3A4_HUMAN267-289231A:270-289 (gaps)20
1.10ENST0000033641110ENSE00001643301chr7:99361638-99361478161CP3A4_HUMAN289-342541A:289-34254
1.11ENST0000033641111ENSE00001651983chr7:99359890-99359664227CP3A4_HUMAN343-418761A:343-41876
1.12ENST0000033641112ENSE00001055100chr7:99358604-99358442163CP3A4_HUMAN418-472551A:418-47255
1.13aENST0000033641113aENSE00001910683chr7:99355851-99355299553CP3A4_HUMAN473-503311A:473-49826

(-) 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
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:455
 aligned with CP3A4_HUMAN | P08684 from UniProtKB/Swiss-Prot  Length:503

    Alignment length:474
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494    
          CP3A4_HUMAN    25 YGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDG 498
               SCOP domains d1w0ga_ A: Mammalian cytochrome P450 3a4                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1w0gA00 A:25-498 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------p450-1w0gA01 A:38-493                                                                                                                                                                                                                                                                                                                                                                                                                                                   ----- Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhhhhhhhh..eeeee..eeeee..hhhhhhhhhh...............hhhhhhh....hhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhh.............hhhhhh........hhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.-------hhhhhh.------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhhh..hhhhhhhhhhhhh....eeeee....eee..eee....eeeeehhhhh............hhhhhh.......................hhhhhhhhhhhhhhhhhh.eeee.......................eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------D---------------------------------------E---------------------V-----------Q-------------------------------Q-------I---H----------S---S----------------------------R---P-----------------------------A----------------------------------------P-------------------------------------------------------N-------------M---------F------------------------------------------L--------------T-------------T---------------------S------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:25-55        Exon 1.3b         ---------------------------------Exon 1.5b  PDB: A:107-144             Exon 1.6a  PDB: A:145-174     -------------------------------------------------Exon 1.8  PDB: A:224-262 UniProt: 224-266  ----------------------Exon 1.10  PDB: A:289-342 UniProt: 289-342            Exon 1.11  PDB: A:343-418 UniProt: 343-418                                  ------------------------------------------------------Exon 1.13a  PDB: A:473-498 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.4  PDB: A:73-106           -------------------------------------------------------------------Exon 1.7  PDB: A:174-224 UniProt: 174-224          ------------------------------------------Exon 1.9 [INCOMPLETE]  --------------------------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:418-472 UniProt: 418-472             -------------------------- Transcript 1 (2)
                 1w0g A  25 YGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLE-------DFLQLMI------------ALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDG 498
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       | -     | 274 |       -    |  294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494    
                                                                                                                                                                                                                                                                       262     270   276          289                                                                                                                                                                                                                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (41, 41)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CP3A4_HUMAN | P08684)
molecular function
    GO:0047638    albendazole monooxygenase activity    Catalysis of the reaction: albendazole + H(+) + NADPH + O(2) = albendazole S-oxide + H(2)O + NADP(+).
    GO:0070330    aromatase activity    Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
    GO:0034875    caffeine oxidase activity    Catalysis of the reaction: caffeine + O2 + 2 H+ + 2 e- = 1,3,7-trimethyluric acid + H2O.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0016712    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced flavin or flavoprotein and one other donor, and one atom of oxygen is incorporated into one donor.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0050591    quinine 3-monooxygenase activity    Catalysis of the reaction: H(+) + NADPH + O(2) + quinine = 3-hydroxyquinine + H(2)O + NADP(+).
    GO:0005496    steroid binding    Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
    GO:0008395    steroid hydroxylase activity    Catalysis of the formation of a hydroxyl group on a steroid by incorporation of oxygen from O2.
    GO:0033780    taurochenodeoxycholate 6alpha-hydroxylase activity    Catalysis of the reactions: taurochenodeoxycholate + NADPH + H+ + O2 = taurohyocholate + NADP+ + H2O, and lithocholate + NADPH + H+ + O2 = hyodeoxycholate + NADP+ + H2O.
    GO:0050649    testosterone 6-beta-hydroxylase activity    Catalysis of the reaction: testosterone + donor-H2 + O2 = 6-beta-hydroxytestosterone + H2O.
    GO:0070576    vitamin D 24-hydroxylase activity    Catalysis of the hydroxylation of C-24 of any form of vitamin D.
    GO:0030343    vitamin D3 25-hydroxylase activity    Catalysis of the reaction: vitamin D3 + NADPH + H+ + O2 = calcidiol + NADP+ + H2O.
biological process
    GO:0009822    alkaloid catabolic process    The chemical reactions and pathways resulting in the breakdown of alkaloids, nitrogen containing natural products not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
    GO:0008209    androgen metabolic process    The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics.
    GO:0036378    calcitriol biosynthetic process from calciol    Conversion of vitamin D3 from its largely inactive form (calciol, also called cholecalciferol) into a hormonally active form (calcitriol). Conversion requires 25-hydroxylation of calciol in the liver to form calcidiol, and subsequent 1,alpha-hydroxylation of calcidiol in the kidney to form calcitriol.
    GO:0042737    drug catabolic process    The chemical reactions and pathways resulting in the breakdown of a drug, a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0017144    drug metabolic process    The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
    GO:0042738    exogenous drug catabolic process    The chemical reactions and pathways resulting in the breakdown of a drug that has originated externally to the cell or organism.
    GO:0046483    heterocycle metabolic process    The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0016098    monoterpenoid metabolic process    The chemical reactions and pathways involving monoterpenoid compounds, terpenoids having a C10 skeleton.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0070989    oxidative demethylation    The process of removing one or more methyl groups from a molecule, involving the oxidation (i.e. electron loss) of one or more atoms in the substrate.
    GO:0006706    steroid catabolic process    The chemical reactions and pathways resulting in the breakdown of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0042359    vitamin D metabolic process    The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
    GO:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031090    organelle membrane    A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CP3A4_HUMAN | P086841tqn 1w0e 1w0f 2j0d 2v0m 3nxu 3tjs 3ua1 4d6z 4d75 4d78 4d7d 4i3q 4i4g 4i4h 4k9t 4k9u 4k9v 4k9w 4k9x 4ny4 5a1p 5a1r 5g5j 5te8 5vc0 5vcc 5vcd 5vce 5vcg

(-) Related Entries Specified in the PDB File

1w0e CRYSTAL STRUCTURE OF HUMAN CYTOCHROME P450 3A4
1w0f CRYSTAL STRUCTURE OF HUMAN CYTOCHROME P450 3A4