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 :  ZN AND ADP BOUND 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 :  2.13
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Zn/Adp-Bound Dimer, 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, B
    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

  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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:112 , CYS A:114BINDING SITE FOR RESIDUE ZN A 255
2AC2SOFTWARELYS A:8 , GLY A:9 , GLY A:10 , VAL A:11 , GLY A:12 , LYS A:13 , THR A:14 , THR A:15 , SER A:40 , ASN A:191 , LYS A:192 , PRO A:216 , TYR A:217 , ASN A:218 , PHE A:221 , SER A:225 , HOH A:361 , HOH A:478BINDING SITE FOR RESIDUE ADP A 256
3AC3SOFTWARECYS B:112 , CYS B:114BINDING SITE FOR RESIDUE ZN B 255
4AC4SOFTWAREARG A:148 , LYS A:184 , LYS B:8 , GLY B:9 , GLY B:10 , VAL B:11 , GLY B:12 , LYS B:13 , THR B:14 , THR B:15 , SER B:40 , ASN B:191 , LYS B:192 , PRO B:216 , TYR B:217 , ASN B:218 , PHE B:221 , HOH B:301 , HOH B:393BINDING SITE FOR RESIDUE ADP B 256

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:112 -B:112

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KJI)

(-) 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: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 .eeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhh..hhhhhhh..hhhhhhhhhhhhhh..........hhhhhhhh.ee....eeeee...........hhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhh...eeeeee..hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhh.eeeeee..hhhhhhhh...........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kji 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    


Chain B 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 (1) -CbiA-3kjiB01 B:2-225                                                                                                                                                                                                            ----------------------------- Pfam domains (1)
           Pfam domains (2) -CbiA-3kjiB02 B:2-225                                                                                                                                                                                                            ----------------------------- Pfam domains (2)
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh.....eeeeee....hhhhhh..hhhhhhhh.hhhhhhhhhhhhhh.............hhhhh.ee....eeeee.............hhhhhhhhhhhhhhhh...eeeeee................eeeeee..hhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kji B   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 3KJI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kji)
 
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
  3kji
    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: 3kje 3kjg 3kjh

(-) Related Entries Specified in the PDB File

3kje 3kjg 3kjh