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 :  EMPTY STATE OF COOC1
 
Authors :  J. -H. Jeoung, H. Dobbek
Date :  03 Nov 09  (Deposition) - 19 Jan 10  (Release) - 09 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Nickel Binding Protein, Atpase, Hydrolase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Jeoung, T. Giese, M. Grunwald, H. Dobbek
Crystal Structure Of The Atp-Dependent Maturation Factor Of Ni, Fe-Containing Carbon Monoxide Dehydrogenases
J. Mol. Biol. V. 396 1165 2010
PubMed-ID: 20064527  |  Reference-DOI: 10.1016/J.JMB.2009.12.062

(-) Compounds

Molecule 1 - CO DEHYDROGENASE/ACETYL-COA SYNTHASE COMPLEX, ACCESSORY PROTEIN COOC
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CHY_1220, COOC1
    Organism Scientific: CARBOXYDOTHERMUS HYDROGENOFORMANS
    Organism Taxid: 246194
    Strain: Z-2901

 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 3KJE)

(-) Sites  (0, 0)

(no "Site" information available for 3KJE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KJE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KJE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KJE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KJE)

(-) Exons   (0, 0)

(no "Exon" information available for 3KJE)

(-) 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:254
 aligned with Q3ACS5_CARHZ | Q3ACS5 from UniProtKB/TrEMBL  Length:254

    Alignment length:254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    
         Q3ACS5_CARHZ     1 MKLAVAGKGGVGKTTVAAGLIKIMASDYDKIYAVDGDPDSCLGQTLGLSIEEAYAITPLIEMKDEIREKTGDGGLLILNPKVDGDLDKYGRYIDDKIFLIRMGEIKKGGSQCYCRENSFLGSVVSALFLDKKEAVVMDMGAGIEHLTRGTAKAVDMMIAVIEPNLNSIKTGLNIEKLAGDLGIKKVRYVINKVRNIKEEKLIKKHLPEDKILGIIPYNELFIELSLKGEEIWQSTNPAFVNLHDIYQKLRLEVG 254
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhh.....eeeeee....hhhhhh..hhhhhhh..hhhhhhhhhhhhhh..........hhhhhhhh.ee....eeeee...........hhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhh...eeeeee..hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhh....eeeeee...................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kje A   1 MKLAVAGKGGVGKTTVAAGLIKIMASDYDKIYAVDGDPDSCLGQTLGLSIEEAYAITPLIEMKDEIREKTGDGGLLILNPKVDGDLDKYGRYIDDKIFLIRMGEIKKGGSQCYCRENSFLGSVVSALFLDKKEAVVMDMGAGIEHLTRGTAKAVDMMIAVIEPNLNSIKTGLNIEKLAGDLGIKKVRYVINKVRNIKEEKLIKKHLPEDKILGIIPYNELFIELSLKGEEIWQSTNPAFVNLHDIYQKLRLEVG 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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 3KJE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KJE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KJE)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q3ACS5_CARHZ | Q3ACS5)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0019415    acetate biosynthetic process from carbon monoxide    The chemical reactions and pathways resulting in the formation of acetate from other compounds, including carbon monoxide.

 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 3kje)
 
  Sites
(no "Sites" information available for 3kje)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kje)
 

(-) 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 ](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
  3kje
    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
  Q3ACS5_CARHZ | Q3ACS5
    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
  Q3ACS5_CARHZ | Q3ACS5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q3ACS5_CARHZ | Q3ACS5: 3kjg 3kjh 3kji

(-) Related Entries Specified in the PDB File

3kje 3kjh 3kji