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(-) Description

Title :  MICROSOMAL CYTOCHROME P450 2C5/3LVDH COMPLEX WITH DICLOFENAC
 
Authors :  M. R. Wester, E. F. Johnson, C. D. Stout
Date :  23 Jan 03  (Deposition) - 12 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Membrane Protein, Progesterone 21-Hydroxylase, Benzo(A), Pyrene Hydroxylase, Estradiol 2-Hydroxylase, P450, Cyp2C5, Diclofenac Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Wester, E. F. Johnson, C. Marques-Soares, S. Dijols, P. M. Dansette, D. Mansuy, C. D. Stout
Structure Of Mammalian Cytochrome P450 2C5 Complexed With Diclofenac At 2. 1 A Resolution: Evidence For An Induced Fit Model Of Substrate Binding
Biochemistry V. 42 9335 2003
PubMed-ID: 12899620  |  Reference-DOI: 10.1021/BI034556L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME P450 2C5
    Chains: A
    EC Number: 1.14.14.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCW
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CYP2C5
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: CYPIIC5, PROGESTERONE 21-HYDROXYLASE, P450 1, P450IIC5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1DIF1Ligand/Ion2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:132 , ASN A:133 , LYS A:454 , HOH A:696 , HOH A:707BINDING SITE FOR RESIDUE SO4 A 502
2AC2SOFTWAREASP A:411 , GLU A:412 , LYS A:417BINDING SITE FOR RESIDUE SO4 A 503
3AC3SOFTWAREARG A:97 , ILE A:112 , TRP A:120 , ARG A:124 , LEU A:291 , ALA A:294 , GLY A:295 , THR A:298 , THR A:302 , LEU A:358 , ASN A:362 , HIS A:365 , PRO A:424 , PHE A:425 , SER A:426 , ARG A:430 , CYS A:432 , GLY A:434 , DIF A:501BINDING SITE FOR RESIDUE HEM A 500
4AC4SOFTWARELEU A:103 , ALA A:113 , PHE A:114 , GLY A:293 , ALA A:294 , THR A:298 , LEU A:359 , LEU A:363 , PHE A:473 , HEM A:500 , HOH A:853 , HOH A:854 , HOH A:856 , HOH A:857BINDING SITE FOR RESIDUE DIF A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NR6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NR6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NR6)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP2C5_RABIT425-434  1A:425-434

(-) Exons   (0, 0)

(no "Exon" information available for 1NR6)

(-) 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:462
 aligned with CP2C5_RABIT | P00179 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      487 
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486| 
          CP2C5_RABIT    27 GKLPPGPTPFPIIGNILQIDAKDISKSLTKFSECYGPVFTVYLGMKPTVVLHGYEAVKEALVDLGEEFAGRGSVPILEKVSKGLGIAFSNAKTWKEMRRFSLMTLRNFGMGKRSIEDRIQEEARCLVEELRKTNASPCDPTFILGCAPCNVICSVIFHNRFDYKDEEFLKLMESLNENVRILSSPWLQVYNNFPALLDYFPGIHKTLLKNADYIKNFIMEKVKEHQKLLDVNNPRDFIDCFLIKMEQENNLEFTLESLVIAVSDLFGAGTETTSTTLRYSLLLLLKHPEVAARVQEEIERVIGRHRSPCMQDRSRMPYTDAVIHEIQRFIDLLPTNLPHAVTRDVRFRNYFIPKGTDIITSLTSVLHDEKAFPNPKVFDPGHFLDESGNFKKSDYFMPFSAGKRMCVGEGLARMELFLFLTSILQNFKLQSLVEPKDLDITAVVNGFVSVPPSYQLCFIPI-   -
               SCOP domains d1nr6a_ A: Mammalian cytochrome p450 2c5                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1nr6A00 A:27-488 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---p450-1nr6A01 A:30-484                                                                                                                                                                                                                                                                                                                                                                                                                                                  ---- Pfam domains
         Sec.struct. author ..............hhhhh...hhhhhhhhhhhhhh.eeeee....eeeee.hhhhhhhhhh.......ee....hhhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeeee..hhhhh....ee....ee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nr6 A  27 GKLPPGPTPFPIIGNILQIDAKDISKSLTKFSECYGPVFTVYLGMKPTVVLHGYEAVKEALVDLGEEFAGRGSVPILEKVSKGLGIAFSNAKTWKEMRRFSLMTLRNFGMGKRSIEDRIQEEARCLVEELRKTNASPCDPTFILGCAPCNVICSVIFHNRFDYKDEEFLKLMESLHENVELLGTPWLQVYNNFPALLDYFPGIHKTLLKNADYIKNFIMEKVKEHQKLLDVNNPRDFIDCFLIKMEQENNLEFTLESLVIAVSDLFGAGTETTSTTLRYSLLLLLKHPEVAARVQEEIERVIGRHRSPCMQDRSRMPYTDAVIHEIQRFIDLLPTNLPHAVTRDVRFRNYFIPKGTDIITSLTSVLHDEKAFPNPKVFDPGHFLDESGNFKKSDYFMPFSAGKRMCVGEGLARMELFLFLTSILQNFKLQSLVEPKDLDITAVVNGFVSVPPSYQLCFIPIH 488
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: p450] (161)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CP2C5_RABIT | P00179)
molecular function
    GO:0070330    aromatase activity    Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
    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.
biological process
    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.
cellular component
    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: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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  1nr6
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  1.14.14.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        CP2C5_RABIT | P00179: 1dt6 1n6b

(-) Related Entries Specified in the PDB File

1dt6 STRUCTURE OF MICROSOMAL CYTOCHROME P450 2C5/3LVDH AT 3.0 A RESOLUTION
1n6b MICROSOMAL CYTOCHROME P450 2C5/3LVDH COMPLEX WITH A DIMETHYL DERIVATIVE OF SULFAPHENAZOLE