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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PLACENTAL AROMATASE COMPLEXED WITH BREAST CANCER DRUG EXEMESTANE
 
Authors :  D. Ghosh
Date :  26 May 11  (Deposition) - 06 Jun 12  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.21
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome P450, Oxidoreductase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Ghosh, J. Lo, D. Morton, D. Valette, J. Xi, J. Griswold, S. Hubbell, C. Egbuta, W. Jiang, J. An, H. M. Davies
Novel Aromatase Inhibitors By Structure-Guided Design.
J. Med. Chem. V. 55 8464 2012
PubMed-ID: 22951074  |  Reference-DOI: 10.1021/JM300930N

(-) Compounds

Molecule 1 - CYTOCHROME P450 19A1
    ChainsA
    EC Number1.14.14.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneCYP19A1, ARO1, CYAR, CYP19
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAROMATASE, CYPXIX, CYTOCHROME P-450AROM, ESTROGEN SYNTHASE

 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
1EXM1Ligand/Ion(8ALPHA,10ALPHA,13ALPHA)-6-METHYLIDENEANDROSTA-1,4-DIENE-3,17-DIONE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:107 , ARG A:115 , ILE A:132 , TRP A:141 , ARG A:145 , ALA A:306 , MET A:364 , VAL A:370 , VAL A:373 , ARG A:375 , PHE A:430 , ARG A:435 , CYS A:437 , MET A:446 , MET A:447 , EXM A:601BINDING SITE FOR RESIDUE HEM A 600
2AC2SOFTWAREARG A:115 , ILE A:133 , TRP A:224 , ALA A:306 , ASP A:309 , THR A:310 , VAL A:370 , LEU A:372 , VAL A:373 , MET A:374 , LEU A:477 , HEM A:600BINDING SITE FOR RESIDUE EXM A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S7S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S7S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Asymmetric/Biological Unit (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_072784R192HCP19A_HUMANDisease (AROD)765057534AR192H
2UniProtVAR_023429T201MCP19A_HUMANPolymorphism28757184AT201M
3UniProtVAR_018406R264CCP19A_HUMANPolymorphism700519AR264C
4UniProtVAR_077526R264HCP19A_HUMANPolymorphism2304462AR264H
5UniProtVAR_016962R365QCP19A_HUMANDisease (AROD)80051519AR365Q
6UniProtVAR_016963R375CCP19A_HUMANDisease (AROD)121434536AR375C
7UniProtVAR_054152R375LCP19A_HUMANPolymorphism  ---AR375L
8UniProtVAR_016964R435CCP19A_HUMANDisease (AROD)121434534AR435C
9UniProtVAR_016965C437YCP19A_HUMANDisease (AROD)78310315AC437Y

  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.CP19A_HUMAN430-439  1A:430-439

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.8bENST000003964048bENSE00001621872chr15:51535147-51534965183CP19A_HUMAN1-49491A:45-495
1.9ENST000003964049ENSE00001685378chr15:51529206-51529056151CP19A_HUMAN49-99511A:49-9951
1.10bENST0000039640410bENSE00001606124chr15:51520130-51519976155CP19A_HUMAN99-151531A:99-15153
1.11aENST0000039640411aENSE00002142222chr15:51514722-51514546177CP19A_HUMAN151-210601A:151-21060
1.12aENST0000039640412aENSE00001767917chr15:51510852-51510738115CP19A_HUMAN210-248391A:210-24839
1.13cENST0000039640413cENSE00001736562chr15:51508014-51507900115CP19A_HUMAN248-286391A:248-28639
1.14ENST0000039640414ENSE00001689208chr15:51507429-51507267163CP19A_HUMAN287-341551A:287-34155
1.15cENST0000039640415cENSE00000688581chr15:51504758-51504517242CP19A_HUMAN341-421811A:341-42181
1.16aENST0000039640416aENSE00000884690chr15:51503253-515002552999CP19A_HUMAN422-503821A:422-49675

(-) 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:452
 aligned with CP19A_HUMAN | P11511 from UniProtKB/Swiss-Prot  Length:503

    Alignment length:452
                                    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  
          CP19A_HUMAN    45 SSIPGPGYCMGIGPLISHGRFLWMGIGSACNYYNRVYGEFMRVWISGEETLIISKSSSMFHIMKHNHYSSRFGSKLGLQCIGMHEKGIIFNNNPELWKTTRPFFMKALSGPGLVRMVTVCAESLKTHLDRLEEVTNESGYVDVLTLLRRVMLDTSNTLFLRIPLDESAIVVKIQGYFDAWQALLIKPDIFFKISWLYKKYEKSVKDLKDAIEVLIAEKRRRISTEEKLEECMDFATELILAEKRGDLTRENVNQCILEMLIAAPDTMSVSLFFMLFLIAKHPNVEEAIIKEIQTVIGERDIKIDDIQKLKVMENFIYESMRYQPVVDLVMRKALEDDVIDGYPVKKGTNIILNIGRMHRLEFFPKPNEFTLENFAKNVPYRYFQPFGFGPRGCAGKYIAMVMMKAILVTLLRRFHVKTLQGQCVESIQKIHDLSLHPDETKNMLEMIFTPRN 496
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhh....hhhhhhhhh..........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhhhhh.................................hhhhhhhhhhhhhhhhhh.eeeee..........eee...eee........eeeee.. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------------------------------------------------------------------------------------------------------------H--------M--------------------------------------------------------------C----------------------------------------------------------------------------------------------------Q---------C-----------------------------------------------------------C-Y----------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------------------------------------------L------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME--------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.8b -------------------------------------------------Exon 1.10b  PDB: A:99-151 UniProt: 99-151            ----------------------------------------------------------Exon 1.12a  PDB: A:210-248             --------------------------------------Exon 1.14  PDB: A:287-341 UniProt: 287-341             --------------------------------------------------------------------------------Exon 1.16a  PDB: A:422-496 UniProt: 422-503 [INCOMPLETE]                    Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.9  PDB: A:49-99 UniProt: 49-99              ---------------------------------------------------Exon 1.11a  PDB: A:151-210 UniProt: 151-210                 -------------------------------------Exon 1.13c  PDB: A:248-286             ------------------------------------------------------Exon 1.15c  PDB: A:341-421 UniProt: 341-421                                      --------------------------------------------------------------------------- Transcript 1 (2)
                 3s7s A  45 SSIPGPGYCMGIGPLISHGRFLWMGIGSACNYYNRVYGEFMRVWISGEETLIISKSSSMFHIMKHNHYSSRFGSKLGLQCIGMHEKGIIFNNNPELWKTTRPFFMKALSGPGLVRMVTVCAESLKTHLDRLEEVTNESGYVDVLTLLRRVMLDTSNTLFLRIPLDESAIVVKIQGYFDAWQALLIKPDIFFKISWLYKKYEKSVKDLKDAIEVLIAEKRRRISTEEKLEECMDFATELILAEKRGDLTRENVNQCILEMLIAAPDTMSVSLFFMLFLIAKHPNVEEAIIKEIQTVIGERDIKIDDIQKLKVMENFIYESMRYQPVVDLVMRKALEDDVIDGYPVKKGTNIILNIGRMHRLEFFPKPNEFTLENFAKNVPYRYFQPFGFGPRGCAGKYIAMVMMKAILVTLLRRFHVKTLQGQCVESIQKIHDLSLHPDETKNMLEMIFTPRN 496
                                    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  

   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  (0, 0)

(no "SCOP Domain" information available for 3S7S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S7S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S7S)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CP19A_HUMAN | P11511)
molecular function
    GO:0070330    aromatase activity    Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    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:0008395    steroid hydroxylase activity    Catalysis of the formation of a hydroxyl group on a steroid by incorporation of oxygen from O2.
biological process
    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:0006703    estrogen biosynthetic process    The chemical reactions and pathways resulting in the formation of estrogens, C18 steroid hormones that can stimulate the development of female sexual characteristics. Also found in plants.
    GO:0002677    negative regulation of chronic inflammatory response    Any process that stops, prevents, or reduces the frequency, rate, or extent of a chronic inflammatory response.
    GO:0010760    negative regulation of macrophage chemotaxis    Any process that decreases the rate, frequency or extent of macrophage chemotaxis. Macrophage chemotaxis is the movement of a macrophage in response to an external stimulus.
    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:0060736    prostate gland growth    The increase in size or mass of the prostate gland where the increase in size or mass has the specific outcome of the progression of the gland, from its formation to its mature state.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0016125    sterol metabolic process    The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CP19A_HUMAN | P115111tqa 3eqm 3s79 4gl5 4gl7 4kq8 5jkv 5jkw 5jl6 5jl7 5jl9

(-) Related Entries Specified in the PDB File

3eqm HUMAN PLACENTAL AROMATASE COMPLEXED WITH THE NATURAL SUBSTRATE ANDROSTENEDIONE AT 2.90 ANGSTROM
3s79 HUMAN PLACENTAL AROMATASE COMPLEXED WITH THE NATURAL SUBSTRATE ANDROSTENEDIONE AT 2.75 ANGSTROM