Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 CHROMOPYRROLIC ACID BOUND CYTOCHROME P450 STAP (CYP245A1)
 
Authors :  M. Makino, H. Sugimoto, Y. Shiro, S. Asamizu, H. Onaka, S. Nagano
Date :  06 Jun 07  (Deposition) - 03 Jul 07  (Release) - 26 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome P450, Monoxygenase, Oxydoreductase, Heme-Enzyme, Chromopyrrolic Acid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Makino, H. Sugimoto, Y. Shiro, S. Asamizu, H. Onaka, S. Nagano
Crystal Structures And Catalytic Mechanism Of Cytochrome P450 Stap That Produces The Indolocarbazole Skeleton
Proc. Natl. Acad. Sci. Usa V. 104 11591 2007
PubMed-ID: 17606921  |  Reference-DOI: 10.1073/PNAS.0702946104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME P450
    Chains: A
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET26B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: STAP
    Organism Scientific: STREPTOMYCES SP. TP-A0274
    Organism Taxid: 171258

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CRR3Ligand/Ion3,4-DI-1H-INDOL-3-YL-1H-PYRROLE-2,5-DICARBOXYLIC ACID
2EDO4Ligand/Ion1,2-ETHANEDIOL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:67 , LEU A:98 , VAL A:99 , HIS A:106 , ARG A:110 , ILE A:161 , LEU A:251 , ALA A:254 , GLY A:255 , THR A:258 , THR A:259 , VAL A:304 , ARG A:306 , GLY A:356 , PHE A:357 , GLY A:358 , ILE A:361 , HIS A:362 , CYS A:364 , LEU A:365 , GLY A:366 , ALA A:370 , GLU A:373 , CRR A:501 , HOH A:776BINDING SITE FOR RESIDUE HEM A 500
2AC2SOFTWAREARG A:67 , TRP A:97 , VAL A:99 , GLN A:183 , SER A:186 , THR A:187 , VAL A:304 , THR A:305 , VAL A:402 , PHE A:403 , HEM A:500 , HOH A:780BINDING SITE FOR RESIDUE CRR A 501
3AC3SOFTWARELYS A:44 , PRO A:45 , THR A:47 , ALA A:69 , ALA A:79 , PRO A:80 , VAL A:81 , PRO A:82 , THR A:305 , TRP A:307 , ARG A:324 , HOH A:780BINDING SITE FOR RESIDUE CRR A 502
4AC4SOFTWAREVAL A:57 , SER A:61 , ARG A:145 , ARG A:353 , LEU A:359 , GLY A:360 , GLU A:394 , ARG A:408 , LEU A:410 , ASP A:412 , HOH A:649 , HOH A:709 , HOH A:753BINDING SITE FOR RESIDUE CRR A 503
5AC5SOFTWARELEU A:11 , GLY A:13 , TRP A:14 , THR A:188 , ASP A:399BINDING SITE FOR RESIDUE EDO A 504
6AC6SOFTWAREARG A:63 , LEU A:65 , HOH A:700BINDING SITE FOR RESIDUE EDO A 505
7AC7SOFTWAREPRO A:103 , HIS A:106 , THR A:107 , HOH A:611BINDING SITE FOR RESIDUE EDO A 506
8AC8SOFTWAREASN A:178 , ALA A:181 , ARG A:198 , ALA A:201 , ALA A:202 , HOH A:718BINDING SITE FOR RESIDUE EDO A 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z3U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:103 -Pro A:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z3U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z3U)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z3U)

(-) 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:411
 aligned with Q83WG3_9ACTN | Q83WG3 from UniProtKB/TrEMBL  Length:417

    Alignment length:411
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413 
         Q83WG3_9ACTN     4 ATLPRFDLMGWDKKDIADPYPVYRRYREAAPVHRTASGPGKPDTYYVFTYDDVVRVLSNRRLGRNARVASGDTDTAPVPIPTEHRALRTVVENWLVFLDPPHHTELRSLLTTEFSPSIVTGLRPRIAELASALLDRLRAQRRPDLVEGFAAPLPILVISALLGIPEEDHTWLRANAVALQEASTTRARDGRGYARAEAASQEFTRYFRREVDRRGGDDRDDLLTLLVRARDTGSPLSVDGIVGTCVHLLTAGHETTTNFLAKAVLTLRAHRDVLDELRTTPESTPAAVEELMRYDPPVQAVTRWAYEDIRLGDHDIPRGSRVVALLGSANRDPARFPDPDVLDVHRAAERQVGFGLGIHYCLGATLARAEAEIGLRALLDGIPALGRGAHEVEYADDMVFHGPTRLLLDLP 414
               SCOP domains d2z3ua_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2z3uA00 A:4-414 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhh...eeee........eeee.hhhhhhhhhhh..ee.hhhhhhh............hhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeeeee...eee..eee....eeeeehhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeee........eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3u A   4 ATLPRFDLMGWDKKDIADPYPVYRRYREAAPVHRTASGPGKPDTYYVFTYDDVVRVLSNRRLGRNARVASGDTDTAPVPIPTEHRALRTVVENWLVFLDPPHHTELRSLLTTEFSPSIVTGLRPRIAELASALLDRLRAQRRPDLVEGFAAPLPILVISALLGIPEEDHTWLRANAVALQEASTTRARDGRGYARAEAASQEFTRYFRREVDRRGGDDRDDLLTLLVRARDTGSPLSVDGIVGTCVHLLTAGHETTTNFLAKAVLTLRAHRDVLDELRTTPESTPAAVEELMRYDPPVQAVTRWAYEDIRLGDHDIPRGSRVVALLGSANRDPARFPDPDVLDVHRAAERQVGFGLGIHYCLGATLARAEAEIGLRALLDGIPALGRGAHEVEYADDMVFHGPTRLLLDLP 414
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413
   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  (0, 0)

(no "Pfam Domain" information available for 2Z3U)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q83WG3_9ACTN | Q83WG3)
molecular function
    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
    CRR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ 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 ]
 
  Cis Peptide Bonds
    Pro A:103 - Pro A:104   [ 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
  2z3u
    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
  Q83WG3_9ACTN | Q83WG3
    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.-.-.-
    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
  Q83WG3_9ACTN | Q83WG3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q83WG3_9ACTN | Q83WG3: 2z3t 3a1l

(-) Related Entries Specified in the PDB File

2z3t THE SAME PROTEIN WITHOUT THE SUBSTRATE