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 :  XANTHOMONAS CAMPESTRIS PEROXIREDOXIN Q - STRUCTURE F9
 
Authors :  A. Perkins, D. Parsonage, K. J. Nelson, L. B. Poole, A. Karplus
Date :  08 Mar 16  (Deposition) - 21 Sep 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Prxq, Bcp, Peroxidase, Redox, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Perkins, D. Parsonage, K. J. Nelson, O. M. Ogba, P. H. Cheong, L. B. Poole, P. A. Karplus
Peroxiredoxin Catalysis At Atomic Resolution.
Structure V. 24 1668 2016
PubMed-ID: 27594682  |  Reference-DOI: 10.1016/J.STR.2016.07.012

(-) Compounds

Molecule 1 - BACTERIOFERRITIN COMIGRATORY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: XCC1738
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS (STRAIN ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)
    Organism Taxid: 190485
    Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CSD1Mod. Amino Acid3-SULFINOALANINE
2NA2Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:18 , HOH A:351 , HOH A:355 , HOH A:440 , HOH A:445 , HOH A:447binding site for residue NA A 201
2AC2SOFTWAREHIS A:30 , HIS A:33 , LEU A:128 , SER A:129 , HOH A:413binding site for residue NA A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IO0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IO0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IO0)

(-) Exons   (0, 0)

(no "Exon" information available for 5IO0)

(-) 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:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh.eee....ee.hhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh....eee...hhhhhhh..eeeeee..eeeeee..eeeee.....eeeeee.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5io0 A   3 DAVLELPAATFDLPLSLSGGTQTTLRAHAGHWLVIYFYPKDSTPGcTTEGLDFNALLPEFDKAGAKILGVSRDSVKSHDNFCAKQGFAFPLVSDGDEALCRAFDVIKEKNMYGKQVLGIERSTFLLSPEGQVVQAWRKVKVAGHADAVLAALKAHAK 159
                                    12        22        32        42     |  52        62        72        82        92       102       112       122       132       142       152       
                                                                        48-CSD
   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 5IO0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IO0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IO0)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CSD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5io0)
 

(-) 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
  5io0
    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
  Q8P9V9_XANCP | Q8P9V9
    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
  Q8P9V9_XANCP | Q8P9V9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8P9V9_XANCP | Q8P9V9: 3gkk 3gkm 3gkn 5im9 5ima 5imc 5imd 5imf 5imv 5imz 5iny 5io2 5iow 5iox 5ipg 5iph

(-) Related Entries Specified in the PDB File

5iiz 5im9 5ima 5imc 5imd 5imf 5imv 5imz 5iny 5io0 5io2 5iow 5iox 5ipg 5iph