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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE COPA C-TERMINAL METAL BINDING DOMAIN
 
Authors :  S. Agarwal, M. Sazinsky, J. Arguello, A. C. Rosenzweig
Date :  08 Jan 09  (Deposition) - 12 Jan 10  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport Protein, Metal Binding Domain, Domain Swap, Atp-Binding, Cell Membrane, Copper Transport, Hydrolase, Ion Transport, Magnesium, Membrane, Metal-Binding, Nucleotide-Binding, Phosphoprotein, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Agarwal, D. Hong, N. K. Desai, M. H. Sazinsky, J. M. Arguello, A. C. Rosenzweig
Structure And Interactions Of The C-Terminal Metal Binding Domain Of Archaeoglobus Fulgidus Copa.
Proteins V. 78 2450 2010
PubMed-ID: 20602459  |  Reference-DOI: 10.1002/PROT.22753

(-) Compounds

Molecule 1 - PROBABLE COPPER-EXPORTING P-TYPE ATPASE A
    Chains: A, B
    EC Number: 3.6.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPR-IBA1
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: AF_0473, COPA, PACS
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Strain: DSM 4304

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:12 , SER A:15 , CYS A:16 , HIS A:17 , HIS A:18 , HOH A:74 , HOH A:99BINDING SITE FOR RESIDUE CIT A2324

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:16 -A:19
2B:16 -B:19

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMA_2PS50846 Heavy-metal-associated domain profile.COPA_ARCFU17-83
741-802
 		  2-
A:6-67
B:6-67
2HMA_1PS01047 Heavy-metal-associated domain.COPA_ARCFU746-774
 		  2A:11-39
B:11-39

(-) Exons   (0, 0)

(no "Exon" information available for 3FRY)

(-) 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:73
 aligned with COPA_ARCFU | O29777 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:73
                                                                                              804    
                                   745       755       765       775       785       795        |-   
           COPA_ARCFU   736 GDSVEKIVLELSGLSCHHCVARVKKALEEAGAKVEKVDLNEAVVAGNKEDVDKYIKAVEAAGYQAKLRS----   -
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee...hhhhhhhhhhhhhhh..eeeee...eeeeeee..hhhhhhhhhhhh..eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----HMA_2  PDB: A:6-67 UniProt: 741-802                           ------ PROSITE (1)
                PROSITE (2) ----------HMA_1  PDB: A:11-39          ---------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------- Transcript
                 3fry A   1 GDSVEKIVLELSGLSCHHCVARVKKALEEAGAKVEKVDLNEAVVAGNKEDVDKYIKAVEAAGYQAKLRSSAWS  73
                                    10        20        30        40        50        60        70   


Chain B from PDB  Type:PROTEIN  Length:72
 aligned with COPA_ARCFU | O29777 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:72
                                                                                             804    
                                   746       756       766       776       786       796       | -  
           COPA_ARCFU   737 DSVEKIVLELSGLSCHHCVARVKKALEEAGAKVEKVDLNEAVVAGNKEDVDKYIKAVEAAGYQAKLRS----   -
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhhhh..eeeee...eeeeeehhhhhhhhhhhhhhh..eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----HMA_2  PDB: B:6-67 UniProt: 741-802                           ------ PROSITE (1)
                PROSITE (2) ---------HMA_1  PDB: B:11-39          ---------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------ Transcript
                 3fry B   2 DSVEKIVLELSGLSCHHCVARVKKALEEAGAKVEKVDLNEAVVAGNKEDVDKYIKAVEAAGYQAKLRSSAWS  73
                                    11        21        31        41        51        61        71
   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 3FRY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (COPA_ARCFU | O29777)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019829    cation-transporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + cation(out) = ADP + phosphate + cation(in).
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0098655    cation transmembrane transport    A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0006811    ion transport    The directed movement of charged atoms or small charged molecules 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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3fry)
 

(-) 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 | Asym./Biol. Unit - sites 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
  3fry
    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
  COPA_ARCFU | O29777
    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)
  3.6.3.-
    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
  COPA_ARCFU | O29777
    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
        COPA_ARCFU | O29777: 2b8e 2hc8 2voy 3a1c 3a1d 3a1e 3j08 3j09

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3FRY)