Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
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 :  COPPER TRAFFICKING: THE SOLUTION STRUCTURE OF BACILLUS SUBTILIS COPZ
 
Authors :  L. Banci, I. Bertini, R. Del Conte, J. Markey, F. J. Ruiz-Duenas
Date :  21 Sep 01  (Deposition) - 19 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Beta-Alpha-Beta-Beta-Alpha-Beta, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Banci, I. Bertini, R. Del Conte, J. Markey, F. J. Ruiz-Duenas
Copper Trafficking: The Solution Structure Of Bacillus Subtilis Copz.
Biochemistry V. 40 15660 2001
PubMed-ID: 11747441  |  Reference-DOI: 10.1021/BI0112715
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COPZ
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21 (DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BSCOPZ
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Other Details: COPZ IS INVOLVED IN THE COPPER TRAFFICKING OF BACILLUS SUBTILIS AND IT DOES BIND COPPER(I) UNDER REDUCING CONDITIONS
    Synonym: PROBABLE MERCURIC ION-BINDING PROTEIN YVGY

 Structural Features

(-) Chains, Units

  
NMR Structure (30x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1CU11Ligand/IonCOPPER (I) ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:13 , CYS A:16BINDING SITE FOR RESIDUE CU1 A 74

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K0V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K0V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K0V)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMA_2PS50846 Heavy-metal-associated domain profile.COPZ_BACSU3-69  1A:3-69
2HMA_1PS01047 Heavy-metal-associated domain.COPZ_BACSU8-37  1A:8-37

(-) Exons   (0, 0)

(no "Exon" information available for 1K0V)

(-) 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:73
 aligned with COPZ_BACSU | O32221 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:73
                                                                                               69    
                                    10        20        30        40        50        60        |-   
            COPZ_BACSU    1 MEQKTLQVEGMSCQHCVKAVETSVGELDGVSAVHVNLEAGKVDVSFDADKVSVKDIADAIEDQGYDVAK----  -
               SCOP domains d1k0va_ A: Copper chaperone                                               SCOP domains
               CATH domains 1k0vA00 A:1-73  [code=3.30.70.100, no name defined]                       CATH domains
               Pfam domains ----HMA-1k0vA01 A:5-66                                            ------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhh.......ee......eeee.......hhhhhhhhhhhhh..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --HMA_2  PDB: A:3-69 UniProt: 3-69                                   ---- PROSITE (1)
                PROSITE (2) -------HMA_1  PDB: A:8-37            ------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------- Transcript
                  1k0v A  1 MEQKTLQVEGMSCQHCVKAVETSVGELDGVSAVHVNLEAGKVDVSFDADKVSVKDIADAIEDQGYDVAKIEGR 73
                                    10        20        30        40        50        60        70
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: HMA] (41)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A   (COPZ_BACSU | O32221)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006825    copper ion transport    The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0030001    metal ion transport    The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    CU1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1k0v)
 

(-) 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
  1k0v
    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
  COPZ_BACSU | O32221
    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)
  (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
  COPZ_BACSU | O32221
    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
        COPZ_BACSU | O32221: 1p8g 2qif 3i9z

(-) Related Entries Specified in the PDB File

1cpz COPPER(I)-LOADED COPZ FROM BACILLUS SUBTILIS. COPZ PROTEIN IS INVOLVED IN THE COPPER TRAFFICKING OF BACILLUS SUBTILIS. COPZ FROM BACILLUS SUBTILIS HAS HIGH HOMOLOGY WITH THAT OF COPZ PROTEIN FROM ENTEROCOCCUS HIRAE.