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

(-) Description

Title :  STRUCTURAL ANALYSIS OF XANTHOMONAS XOPD PROVIDES INSIGHTS INTO SUBSTRATE SPECIFICITY OF UBIQUITIN-LIKE PROTEIN PROTEASES
 
Authors :  R. Chosed, D. R. Tomchick, C. A. Brautigam, M. Machius, K. Orth
Date :  11 Jan 07  (Deposition) - 29 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Clan Ce Family 48 Cysteine Protease, Type Iii Secreted Effector, Desumoylating Enzyme, Secreted Virulence Factor, Peptidase, Isopeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Chosed, D. R. Tomchick, C. A. Brautigam, S. Mukherjee, V. S. Negi, M. Machius, K. Orth
Structural Analysis Of Xanthomonas Xopd Provides Insights Into Substrate Specificity Of Ubiquitin-Like Protein Proteases.
J. Biol. Chem. V. 282 6773 2007
PubMed-ID: 17204475  |  Reference-DOI: 10.1074/JBC.M608730200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - XANTHOMONAS OUTER PROTEIN D
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-RTEV
    Expression System Strain: BL21/DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC FRAGMENT (RESIDUES 335-520)
    Gene: XOPD
    Organism Scientific: XANTHOMONAS EUVESICATORIA
    Organism Taxid: 456327

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:35 , ASN A:360 , ARG A:418 , VAL A:485 , GLY A:488 , ASP A:491BINDING SITE FOR RESIDUE PO4 A 100

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OIV)

(-) Exons   (0, 0)

(no "Exon" information available for 2OIV)

(-) 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:170
 aligned with Q3BYJ5_XANC5 | Q3BYJ5 from UniProtKB/TrEMBL  Length:545

    Alignment length:177
                                   347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       
         Q3BYJ5_XANC5   338 WLLDGHLRAYTDDLARRLRGEPNAHLLHFADSQVVTMLSSADPDQQARAQRLLAGDDIPPIVFLPINQPNAHWSLLVVDRRNKDAVAAYHYDSMAQKDPQQRYLADMAAYHLGLDYQQTHEMPIAIQSDGYSCGDHVLTGIEVLAHRVLDGTFDYAGGRDLTDIEPDRGLIRDRLAQ 514
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Peptidase_C48-2oivA01 A:338-514                                                                                                                                                   Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...hhh.eee.hhhhhhhh...hhhhhhhhhhhhhh.....eeeeeeee...eeeeeeee.......eeeee...--..hhhhhhhhhhhhhh..hhhhheee....-----hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oiv A 338 WLLDGHLRAYTDDLARRLRGEPNAHLLHFADSQVVTMLSSADPDQQARAQRLLAGDDIPPIVFLPINQPNAHWSLLVVDRRNKDAVAAYHYDSM--KDPQQRYLADMAAYHLGLDYQQTHEMPIAI-----SCGDHVLTGIEVLAHRVLDGTFDYAGGRDLTDIEPDRGLIRDRLAQ 514
                                   347       357       367       377       387       397       407       417       427   |  |437       447       457     |   - |     477       487       497       507       
                                                                                                                       431  |                          463   469                                             
                                                                                                                          434
   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 2OIV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_CE (7)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q3BYJ5_XANC5 | Q3BYJ5)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

 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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2oiv)
 

(-) 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
  2oiv
    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
  Q3BYJ5_XANC5 | Q3BYJ5
    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
  Q3BYJ5_XANC5 | Q3BYJ5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q3BYJ5_XANC5 | Q3BYJ5: 2oix 5jp1 5jp3

(-) Related Entries Specified in the PDB File

2oix