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 7-CYANO-7-DEAZAGUANINE REDUCTASE, QUEF FROM VIBRIO CHOLERAE O1 BIOVAR EL TOR COMPLEXED WITH CYTOSINE
 
Authors :  Y. Kim, M. Zhou, M. Gu, W. F. Anderson, A. Joachimiak, Center For Struc Genomics Of Infectious Diseases (Csgid)
Date :  11 Jan 13  (Deposition) - 23 Jan 13  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, Tunneling Fold, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Zhou, M. Gu, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of 7-Cyano-7-Deazaguanine Reductase, Quef From Vibrio Cholerae O1 Biovar El Tor Complexed With Cytosine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NADPH-DEPENDENT 7-CYANO-7-DEAZAGUANINE REDUCTASE
    Chains: A, B
    EC Number: 1.7.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: QUEF, VCM66_0859
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961
    Synonym: 7-CYANO-7-CARBAGUANINE REDUCTASE, NADPH-DEPENDENT NITRILE OXIDOREDUCTASE, PREQ(0) REDUCTASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CYT2Ligand/Ion6-AMINOPYRIMIDIN-2(1H)-ONE
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CYT2Ligand/Ion6-AMINOPYRIMIDIN-2(1H)-ONE
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CYT2Ligand/Ion6-AMINOPYRIMIDIN-2(1H)-ONE
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:62 , LEU A:92 , ILE A:93 , SER A:95 , HIS A:233 , GLU A:234 , ILE A:267BINDING SITE FOR RESIDUE CYT A 301
2AC2SOFTWAREGLY A:263 , HOH A:455BINDING SITE FOR RESIDUE CL A 302
3AC3SOFTWARETRP B:62 , ILE B:93 , SER B:95 , ILE B:196 , PHE B:232 , HIS B:233 , GLU B:234BINDING SITE FOR RESIDUE CYT B 301
4AC4SOFTWAREARG B:262 , GLY B:263BINDING SITE FOR RESIDUE CL B 302
5AC5SOFTWAREPHE B:167 , ASP B:168 , ASP B:169 , HOH B:588 , HOH B:602BINDING SITE FOR RESIDUE SO4 B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IQI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IQI)

(-) 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.eeehhhhhhhh........eeeeeeeeeeeeee.....eeeeeeeeeee....eeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........ee.............hhhhhh..eeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeehhhhhhhhhhh....eehhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iqi A  29 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNCLITNQPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRmARQ 287
                                    38        48        58        68        78        88        98       108       118       128       138       148 |     158       168       178       188       198       208     | 218       228       238      |248       258       268       278     |   
                                                                                                                                                   150-MSE                                                         214-MSE                        245-MSE                                284-MSE


Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.eeehhhhhhhhh.......eeeeeeeeeeeeee.....eeeeeeeeeee....eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...eeeeehhhhhh.........ee.............hhhhhh..eeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeehhhhhhhhhhh....eehhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iqi B  29 NQYDPSLLQPVPRSLNRNDLHLSATLPFQGCDIWTLYELSWLNQKGLPQVAIGEVSIPATSANLIESKSFKLYLNSYNQTRFASWDEVQTRLVHDLSACAGETVTVNVKSLNEYTAEPIVTmQGECIDDQDIEIANYEFDDALLQGAAQGEEVSEVLHSHLLKSNCLITNQPDWGSVEIAYHGAKmNREALLRYLVSFREHNEFHEQCVERIFTDImRYCQPQSLTVYARYTRRGGLDINPFRSSHQSAPNHNQRmARQ 287
                                    38        48        58        68        78        88        98       108       118       128       138       148 |     158       168       178       188       198       208     | 218       228       238      |248       258       268       278     |   
                                                                                                                                                   150-MSE                                                         214-MSE                        245-MSE                                284-MSE
   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 4IQI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 15)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CYT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4iqi)
 
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
  4iqi
    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
  C3LTF1_VIBCM | C3LTF1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  QUEF_VIBCH | Q9KTK0
    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)
  1.7.1.13
    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
  C3LTF1_VIBCM | C3LTF1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  QUEF_VIBCH | Q9KTK0
    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
        C3LTF1_VIBCM | C3LTF1: 3uxj 3uxv
        QUEF_VIBCH | Q9KTK0: 3bp1 3rj4 3rzp 3s19 3uxj 3uxv 4ghm

(-) Related Entries Specified in the PDB File

3bp1 THE SAME PROTEIN COMPLEXED WITH GUANINE
3rj4 THE SAME PROTEIN WITHOUT ANY LIGAND BOUND RELATED ID: CSGID-IDP01750 RELATED DB: TARGETTRACK