Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF ZN(II)COX4
 
Authors :  J. H. Coyne Iii, S. Ciofi-Baffoni
Date :  27 Dec 06  (Deposition) - 09 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (21x)
Keywords :  All Beta-Protein, Metallo-Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Coyne, S. Ciofi-Baffoni, L. Banci, I. Bertini, L. Zhang, G. N. George, D. R. Winge
The Characterization And Role Of Zinc Binding In Yeast Cox4.
J. Biol. Chem. V. 282 8926 2007
PubMed-ID: 17215247  |  Reference-DOI: 10.1074/JBC.M610303200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C OXIDASE POLYPEPTIDE IV
    Chains: A
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET20B+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: COX4 SUBUNIT
    Gene: COX4
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  
NMR Structure (21x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:111 , HIS A:119 , MET A:122 , CYS A:134 , CYS A:137BINDING SITE FOR RESIDUE ZN A 156

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ODX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ODX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ODX)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COX5B_1PS00848 Cytochrome c oxidase subunit Vb, zinc binding region signature.COX4_YEAST121-143  1A:121-143

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL187C1YGL187C.1VII:150177-149710468COX4_YEAST1-1551551A:94-14754

(-) Sequences/Alignments

NMR Structure
   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:54
 aligned with COX4_YEAST | P04037 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:54
                                   103       113       123       133       143    
           COX4_YEAST    94 MKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNPVG 147
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains COX5B-2odxA01 A:94-147                                 Pfam domains
         Sec.struct. author .....ee........eee..........eee......eee......eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------COX5B_1  PDB: A:121-143---- PROSITE
               Transcript 1 Exon 1.1  PDB: A:94-147 UniProt: 1-155 [INCOMPLETE]    Transcript 1
                 2odx A  94 MKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNPVG 147
                                   103       113       123       133       143
   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 2ODX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ODX)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Rubredoxin (46)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (COX4_YEAST | P04037)
molecular function
    GO:0004129    cytochrome-c oxidase activity    Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009060    aerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
    GO:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    GO:0006123    mitochondrial electron transport, cytochrome c to oxygen    The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
    GO:0033617    mitochondrial respiratory chain complex IV assembly    The aggregation, arrangement and bonding together of a set of components to form respiratory chain complex IV (also known as cytochrome c oxidase) in the mitochondrial inner membrane.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006119    oxidative phosphorylation    The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005740    mitochondrial envelope    The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005751    mitochondrial respiratory chain complex IV    A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2).
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

 Visualization

(-) Interactive Views

NMR Structure
  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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2odx)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  2odx
    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
  COX4_YEAST | P04037
    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)
  1.9.3.1
    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
  COX4_YEAST | P04037
    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
        COX4_YEAST | P04037: 1hr8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2ODX)