Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF NITROSYL CYTOCHROME P450CIN
 
Authors :  Y. Madrona, S. M. Tripathi, H. Li, T. L. Poulos
Date :  05 Jul 12  (Deposition) - 25 Jul 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  P450, Heme, Monooxygenase, Cindoxin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Madrona, S. Tripathi, H. Li, T. L. Poulos
Crystal Structures Of Substrate-Free And Nitrosyl Cytochrom P450Cin: Implications For O(2) Activation.
Biochemistry V. 51 6623 2012
PubMed-ID: 22775403  |  Reference-DOI: 10.1021/BI300666U

(-) Compounds

Molecule 1 - P450CIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCWORI-P450CIN
    Expression System Strain: DH5-ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 8-404
    Gene: CIN A, CINA
    Organism Scientific: CITROBACTER BRAAKII
    Organism Taxid: 57706

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1CNL2Ligand/Ion1,3,3-TRIMETHYL-2-OXABICYCLO[2.2.2]OCTANE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3NO2Ligand/IonNITRIC OXIDE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1CNL1Ligand/Ion1,3,3-TRIMETHYL-2-OXABICYCLO[2.2.2]OCTANE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3NO-1Ligand/IonNITRIC OXIDE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1CNL1Ligand/Ion1,3,3-TRIMETHYL-2-OXABICYCLO[2.2.2]OCTANE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3NO-1Ligand/IonNITRIC OXIDE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:73 , VAL A:76 , MET A:90 , ALA A:91 , HIS A:98 , ARG A:102 , PHE A:109 , ILE A:234 , GLY A:238 , ASN A:242 , THR A:243 , PHE A:246 , ARG A:289 , PHE A:312 , SER A:339 , LEU A:340 , GLY A:341 , ILE A:344 , HIS A:345 , CYS A:347 , LEU A:348 , CNL A:502 , NO A:503 , HOH A:617BINDING SITE FOR RESIDUE HEM A 501
02AC2SOFTWARETHR A:77 , TYR A:81 , LEU A:237 , ASN A:242 , MET A:286 , HEM A:501 , NO A:503BINDING SITE FOR RESIDUE CNL A 502
03AC3SOFTWAREGLY A:238 , ASN A:242 , HEM A:501 , CNL A:502BINDING SITE FOR RESIDUE NO A 503
04AC4SOFTWAREGLY A:50 , GLY A:51 , LYS A:303 , PRO A:304 , GLY A:305 , GLN A:306 , PEG A:505BINDING SITE FOR RESIDUE PG4 A 504
05AC5SOFTWARETRP A:45 , PG4 A:504BINDING SITE FOR RESIDUE PEG A 505
06AC6SOFTWAREASN B:73 , VAL B:76 , MET B:90 , ALA B:91 , HIS B:98 , ARG B:102 , ILE B:234 , LEU B:235 , GLY B:238 , ASN B:242 , THR B:243 , PRO B:284 , ARG B:289 , PHE B:312 , SER B:339 , LEU B:340 , GLY B:341 , ILE B:344 , HIS B:345 , CYS B:347 , LEU B:348 , ILE B:353 , CNL B:502 , NO B:503 , HOH B:648BINDING SITE FOR RESIDUE HEM B 501
07AC7SOFTWARELEU B:237 , ASN B:242 , MET B:286 , HEM B:501 , NO B:503BINDING SITE FOR RESIDUE CNL B 502
08AC8SOFTWAREGLY B:238 , ASN B:242 , HEM B:501 , CNL B:502BINDING SITE FOR RESIDUE NO B 503
09AC9SOFTWAREGLY B:50 , GLY B:51 , LYS B:303 , PRO B:304 , GLY B:305 , GLN B:306 , PEG B:505 , HOH B:626BINDING SITE FOR RESIDUE PG4 B 504
10BC1SOFTWAREPG4 B:504BINDING SITE FOR RESIDUE PEG B 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FYZ)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:78 -Pro A:79
2Asp A:95 -Pro A:96
3Thr A:333 -Pro A:334
4Phe B:78 -Pro B:79
5Asp B:95 -Pro B:96
6Thr B:333 -Pro B:334

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FYZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FYZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4FYZ)

(-) Sequences/Alignments

Asymmetric 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:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhh...eeeehhhhheeee.hhhhhhhhhhh...ee.......................hhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhh.....eeehhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeee...eee..eee....eeeehhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee......eee.....eeee.eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyz A   8 TSLFTTADHYHTPLGPDGTPHAFFEALRDEAETTPIGWSEAYGGHWVVAGYKEIQAVIQNTKAFSNKGVTFPRYETGEFELMMAGQDDPVHKKYRQLVAKPFSPEATDLFTEQLRQSTNDLIDARIELGEGDAATWLANEIPARLTAILLGLPPEDGDTYRRWVWAITHVENPEEGAEIFAELVAHARTLIAERRTNPGNDIMSRVIMSKIDGESLSEDDLIGFFTILLLGGIDNTARFLSSVFWRLAWDIELRRRLIAHPELIPNAVDELLRFYGPAMVGRLVTQEVTVGDITMKPGQTAMLWFPIASRDRSAFDSPDNIVIERTPNRHLSLGHGIHRCLGAHLIRVEARVAITEFLKRIPEFSLDPNKECEWLMGQVAGMLHVPIIFPKGKRLSE 404
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       


Chain B from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhh...eeeehhhhheeee.hhhhhhhhhhh...ee.......................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....eeehhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeee...eee..eee....eeeehhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee......eee.....eeee.eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyz B   8 TSLFTTADHYHTPLGPDGTPHAFFEALRDEAETTPIGWSEAYGGHWVVAGYKEIQAVIQNTKAFSNKGVTFPRYETGEFELMMAGQDDPVHKKYRQLVAKPFSPEATDLFTEQLRQSTNDLIDARIELGEGDAATWLANEIPARLTAILLGLPPEDGDTYRRWVWAITHVENPEEGAEIFAELVAHARTLIAERRTNPGNDIMSRVIMSKIDGESLSEDDLIGFFTILLLGGIDNTARFLSSVFWRLAWDIELRRRLIAHPELIPNAVDELLRFYGPAMVGRLVTQEVTVGDITMKPGQTAMLWFPIASRDRSAFDSPDNIVIERTPNRHLSLGHGIHRCLGAHLIRVEARVAITEFLKRIPEFSLDPNKECEWLMGQVAGMLHVPIIFPKGKRLSE 404
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397
   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 4FYZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FYZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FYZ)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    CNL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ 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
    Asp A:95 - Pro A:96   [ RasMol ]  
    Asp B:95 - Pro B:96   [ RasMol ]  
    Phe A:78 - Pro A:79   [ RasMol ]  
    Phe B:78 - Pro B:79   [ RasMol ]  
    Thr A:333 - Pro A:334   [ RasMol ]  
    Thr B:333 - Pro B:334   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4fyz
    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
  CINA_CITBR | Q8VQF6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  CINA_CITBR | Q8VQF6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CINA_CITBR | Q8VQF6: 1t2b 3bdz 3be0 4fb2 4fmx 4l6g 4l77 4lht

(-) Related Entries Specified in the PDB File

4fb2 P450CIN SUBSTRATE-FREE
4fmx P450CIN SUBSTRATE-BOUND
4g3r