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 A PUTATIVE NITROREDUCTASE FROM GEOBACTER SULFURREDUCENS PCA (TARGET PSI-013445)
 
Authors :  P. R. Kumar, R. Bhosle, B. Hillerich, R. Seidel, R. Toro, S. C. Almo, New Structural Genomics Research Consortium (Nysgrc)
Date :  23 Jul 12  (Deposition) - 08 Aug 12  (Release) - 08 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium (Nysgrc), Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Kumar, M. Ahmed, N. Banu, R. Bhosle, J. Bonanno, S. Chamala, S. Chowdhury, A. Gizzi, S. Glen, J. Hammonds, B. Hillerich, J. D. Love, R. Seidel, M. Stead, R. Toro, E. Washington, S. C. Almo, New York Structural Genomics Research Consortium (Nysgrc)
Crystal Structure Of A Nitroreductase From Geobacter Sulfurreducens Pca
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NITROREDUCTASE FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GSU0217
    Organism Scientific: GEOBACTER SULFURREDUCENS
    Organism Taxid: 243231
    Strain: PCA, ATCC 51573

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2GOL1Ligand/IonGLYCEROL
3MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:10 , ARG A:11 , SER A:12 , ARG A:14 , TYR A:74 , ASN A:77 , PRO A:78 , ALA A:79 , PHE A:132 , VAL A:133 , GLY A:134 , VAL A:135 , HOH A:430 , HOH A:442 , PRO B:37 , SER B:38 , TRP B:39 , ASN B:41 , PHE B:68 , ASP B:111 , ILE B:114 , PRO B:172 , ARG B:174BINDING SITE FOR RESIDUE FMN A 300
2AC2SOFTWAREPRO A:37 , SER A:38 , TRP A:39 , ASN A:41 , ASP A:111 , PRO A:172 , ARG A:174 , ARG B:10 , ARG B:11 , SER B:12 , ARG B:14 , TYR B:74 , ASN B:77 , PRO B:78 , ALA B:79 , PHE B:132 , VAL B:133 , GLY B:134 , VAL B:135 , HOH B:328BINDING SITE FOR RESIDUE FMN B 201
3AC3SOFTWAREVAL B:95 , PRO B:96 , GLY B:97 , GLU B:150 , ILE B:151BINDING SITE FOR RESIDUE GOL B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G8S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G8S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G8S)

(-) Exons   (0, 0)

(no "Exon" information available for 4G8S)

(-) 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:182
                                                                                                                                                                                                                      
               SCOP domains d4g8sa_ A: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhh..hhhhh........hhhhhhhh.eeeeeee.hhhh.ee..eehhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhh.....eeeeeeeee.......hhhhheee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8s A  -2 FQSmDTLEAIRTRRSVRAFSDRPVEPEKLQmVLEAARQAPSWANmQCSRFVVVQDAEVKAKISELSFVEAFFAPLGYRTNPAQKALAEAPVVIVACGVPGESGDLRGQQYYmTDVGIATENLmLAAHAVGLGSVFVGVFGEEQLGDLLDIPPEIRIVGLFPLGYPRPARKPLDEIVFQGKWK 187
                               |     7        17        27|       37    |   47        57        67        77        87        97       107 |     117  |    127       137       147       157     ||175       185  
                               |                         28-MSE        42-MSE                                                            109-MSE    120-MSE                                    163|               
                               1-MSE                                                                                                                                                            172               


Chain B from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains d4g8sb_ B: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...........hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhh...hhhhh........hhhhhhhh.eeeeeee.hhhh.ee..eehhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhh.....eeeeeeeee.........hhhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8s B   0 SmDTLEAIRTRRSVRAFSDRPVEPEKLQmVLEAARQAPSWANmQCSRFVVVQDAEVKAKISELSFVEAFFAPLGYRTNPAQKALAEAPVVIVACGVPGESGDLRGQQYYmTDVGIATENLmLAAHAVGLGSVFVGVFGEEQLGDLLDIPPEIRIVGLFPLGYPRSGPARKPLDEIVFQGKW 186
                             |       9        19        29        39  |     49        59        69        79        89        99       109       119|      129       139       149       159   ||  175       185 
                             1-MSE                     28-MSE        42-MSE                                                            109-MSE    120-MSE                                    163|                
                                                                                                                                                                                              170
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G8S)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4g8s)
 

(-) 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
  4g8s
    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
  Q74GM9_GEOSL | Q74GM9
    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)
  (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
  Q74GM9_GEOSL | Q74GM9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4G8S)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4G8S)