Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS CYP164A2 WITH ECONAZOLE BOUND
 
Authors :  C. R. J. Agnew, S. L. Kelly, R. L. Brady
Date :  25 Mar 11  (Deposition) - 28 Mar 12  (Release) - 08 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome P450, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Agnew, A. G. Warrilow, N. M. Burton, D. C. Lamb, S. L. Kelly, R. L. Brady
An Enlarged, Adaptable Active Site In Cyp164 Family P450 Enzymes, The Sole P450 In Mycobacterium Leprae.
Antimicrob. Agents Chemother. V. 56 391 2012
PubMed-ID: 22037849  |  Reference-DOI: 10.1128/AAC.05227-11

(-) Compounds

Molecule 1 - CYTOCHROME P450 164A2
    Chains: A
    EC Number: 1.14.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: ATCC 700084

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1ECL2Ligand/Ion1-[(2R)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE
2EDO6Ligand/Ion1,2-ETHANEDIOL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4NA1Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:105 , ARG A:109 , PHE A:116 , ILE A:159 , LEU A:252 , LEU A:253 , ALA A:256 , THR A:260 , LEU A:264 , MET A:297 , VAL A:303 , ARG A:308 , GLY A:358 , PHE A:359 , GLY A:360 , ALA A:363 , HIS A:364 , CYS A:366 , GLY A:368 , ALA A:372 , NA A:425 , HOH A:442 , ECL A:451BINDING SITE FOR RESIDUE HEM A 450
02AC2SOFTWAREALA A:95 , LEU A:184 , ILE A:255 , ALA A:256 , THR A:260 , VAL A:303 , LEU A:305 , VAL A:306 , THR A:403 , HEM A:450 , ECL A:452BINDING SITE FOR RESIDUE ECL A 451
03AC3SOFTWARESER A:71 , PRO A:94 , ALA A:95 , LEU A:98 , LEU A:100 , VAL A:112 , ALA A:248 , THR A:249 , ASN A:251 , LEU A:367 , NA A:425 , ECL A:451BINDING SITE FOR RESIDUE ECL A 452
04AC4SOFTWAREARG A:288 , ASP A:350BINDING SITE FOR RESIDUE EDO A 419
05AC5SOFTWAREPRO A:89 , ILE A:354 , ARG A:355BINDING SITE FOR RESIDUE EDO A 420
06AC6SOFTWARELEU A:64 , HIS A:66 , SER A:69 , HIS A:364 , GLU A:397BINDING SITE FOR RESIDUE EDO A 421
07AC7SOFTWAREGLY A:224 , GLU A:225 , ASP A:226BINDING SITE FOR RESIDUE EDO A 422
08AC8SOFTWAREPRO A:47 , ASN A:50BINDING SITE FOR RESIDUE EDO A 423
09AC9SOFTWAREGLU A:143 , PHE A:144 , ASN A:145 , SER A:411BINDING SITE FOR RESIDUE EDO A 424
10BC1SOFTWAREHIS A:105 , HIS A:364 , HEM A:450 , ECL A:452BINDING SITE FOR RESIDUE NA A 425

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R9C)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:141 -Pro A:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R9C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R9C)

(-) Exons   (0, 0)

(no "Exon" information available for 3R9C)

(-) 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:400
 aligned with A0R5U2_MYCS2 | A0R5U2 from UniProtKB/TrEMBL  Length:414

    Alignment length:400
                                    24        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
         A0R5U2_MYCS2    15 AQGLLLQLLDPATRADPYPIYDRIRRGGPLALPEANLAVFSSFSDCDDVLRHPSSCSDRTKSTIFQRQLAAETQPRPQGPASFLFLDPPDHTRLRGLVSKAFAPRVIKRLEPEITALVDQLLDAVDGPEFNLIDNLAYPLPVAVICRLLGVPIEDEPKFSRASALLAAALDPFLALTGETSDLFDEQMKAGMWLRDYLRALIDERRRTPGEDLMSGLVAVEESGDQLTEDEIIATCNLLLIAGHETTVNLIANAALAMLRTPGQWAALAADGSRASAVIEETMRYDPPVQLVSRYAGDDLTIGTHTVPKGDTMLLLLAAAHRDPTIVGAPDRFDPDRAQIRHLGFGKGAHFCLGAPLARLEATVALPALAARFPEARLSGEPEYKRNLTLRGMSTLSIAV 414
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhh..eeehhh.eeee.hhhhhhhhhhh..ee.hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhh.....eeeee...eee..eee....eeeehhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee....ee........eee.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r9c A  15 AQGLLLQLLDPATRADPYPIYDRIRRGGPLALPEANLAVFSSFSDCDDVLRHPSSCSDRTKSTIFQRQLAAETQPRPQGPASFLFLDPPDHTRLRGLVSKAFAPRVIKRLEPEITALVDQLLDAVDGPEFNLIDNLAYPLPVAVICRLLGVPIEDEPKFSRASALLAAALDPFLALTGETSDLFDEQMKAGMWLRDYLRALIDERRRTPGEDLMSGLVAVEESGDQLTEDEIIATCNLLLIAGHETTVNLIANAALAMLRTPGQWAALAADGSRASAVIEETMRYDPPVQLVSRYAGDDLTIGTHTVPKGDTMLLLLAAAHRDPTIVGAPDRFDPDRAQIRHLGFGKGAHFCLGAPLARLEATVALPALAARFPEARLSGEPEYKRNLTLRGMSTLSIAV 414
                                    24        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
   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 3R9C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R9C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R9C)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A0R5U2_MYCS2 | A0R5U2)
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ECL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:141 - Pro A:142   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3r9c
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A0R5U2_MYCS2 | A0R5U2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.14.-.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  A0R5U2_MYCS2 | A0R5U2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0R5U2_MYCS2 | A0R5U2: 3r9b

(-) Related Entries Specified in the PDB File

3r9b THE ENZYME IN LIGAND FREE STATE