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

(-) Description

Title :  PUTATIVE MOLYBDOPTERIN CONVERTING FACTOR, SUBUNIT 1 FROM PYROCOCCUS FURIOSUS, PFU-562899-001
 
Authors :  L. Chen, Z. J. Liu, W. Tempel, A. Shah, D. Lee, J. P. Rose, J. C. Eneh, R. C. H F. E. Jenney Jr. , H. S. Lee, T. Li, F. L. Poole Ii, C. Shah, F. J. Sugar, M. W. W. Adams, D. C. Richardson, J. S. Richardson, B. C. Wang, Southeas Collaboratory For Structural Genomics (Secsg)
Date :  10 Mar 04  (Deposition) - 10 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Molybdopterin Converting Factor, Subunit 1, Pfu- 562899-001, Pyrococcus Furiosus, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Chen, Z. J. Liu, W. Tempel, A. Shah, D. Lee, J. P. Rose, J. C. Eneh, R. C. Hopkins, F. E. Jenney Jr. , H. S. Lee, T. Li, F. L. Poole Ii, C. Shah F. J. Sugar, M. W. W. Adams, D. C. Richardson, J. S. Richardson, B. C. Wang, Southeast Collaboratory For Structural Genomics
Putative Molybdopterin Converting Factor, Subunit 1 From Pyrococcus Furiosus, Pfu-562899-001 '
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MOLYBDOPTERIN CONVERTING FACTOR, SUBUNIT 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificPYROCOCCUS FURIOSUS
    Organism Taxid2261
    Other DetailsTHE PROTEIN WAS CLONED, EXPRESSED AND PURIFIED BY THE SECSG PYROCOCCUS PROTEIN PRODUCTION GROUP (M.W.W.ADAMS, P.S.BRERETON, M.IZUMI, F.E.JENNEY JR., H.- S.LEE, F.L.POOLE II, C.SHAH, F.SUGAR) UNDER THE DIRECTION OF M.W.W.ADAMS.

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VJK)

(-) Sites  (0, 0)

(no "Site" information available for 1VJK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VJK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VJK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VJK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VJK)

(-) Exons   (0, 0)

(no "Exon" information available for 1VJK)

(-) 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:88
 aligned with Q8U3C7_PYRFU | Q8U3C7 from UniProtKB/TrEMBL  Length:90

    Alignment length:88
                                    10        20        30        40        50        60        70        80        
          Q8U3C7_PYRFU    1 MVKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWDEELKDGDVVGVFPPVS 88
               SCOP domains d1vjka_ A: Molybdopterin synthase subunit MoaD                                           SCOP domains
               CATH domains 1vjkA00 A:1-88  [code=3.10.20.30, no name defined]                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhh............eeee...............eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  1vjk A  1 SVKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWDEELKDGDVVGVFPPVS 88
                                    10        20        30        40        50        60        70        80        

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VJK)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8U3C7_PYRFU | Q8U3C7)
biological process
    GO:0006777    Mo-molybdopterin cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.

 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
(no "Ligands, Modified Residues, Ions" information available for 1vjk)
 
  Sites
(no "Sites" information available for 1vjk)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vjk)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1vjk
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8U3C7_PYRFU | Q8U3C7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q8U3C7_PYRFU | Q8U3C7
    Protein Disorder PredictionDisEMBL | 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 1VJK)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VJK)