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 :  INSIGHTS INTO THE ALKYL PEROXIDE REDUCTION ACTIVITY OF XANTHOMONAS CAMPESTRIS BACTERIOFERRITIN COMIGRATORY PROTEIN FROM THE TRAPPED INTERMEDIATE/LIGAND COMPLEX STRUCTURES
 
Authors :  S. -J. Liao
Date :  11 Mar 09  (Deposition) - 16 Jun 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A
Keywords :  Xanthomonas Campestris, Bcp, Prx, Atypical 2-Cys, Crystal Structure, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. -J. Liao, C. -Y. Yang, K. -H. Chin, A. H. -J. Wang, S. -H. Chou
Insights Into The Alkyl Peroxide Reduction Pathway Of Xanthomonas Campestris Bacterioferritin Comigratory Protein From The Trapped Intermediate-Ligand Complex Structures
J. Mol. Biol. V. 390 951 2009
PubMed-ID: 19477183  |  Reference-DOI: 10.1016/J.JMB.2009.05.030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIOFERRITIN COMIGRATORY PROTEIN
    Chains: A
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BCP
    Mutation: YES
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
    Organism Taxid: 340
    Strain: 17

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1FMT12Ligand/IonFORMIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:90 , HOH A:391BINDING SITE FOR RESIDUE FMT A 408
02AC2SOFTWAREVAL A:5 , LEU A:6 , ALA A:137 , ARG A:139 , HOH A:347BINDING SITE FOR RESIDUE FMT A 409
03AC3SOFTWARESER A:18 , SER A:95 , GLY A:97 , HOH A:269 , FMT A:415BINDING SITE FOR RESIDUE FMT A 410
04AC4SOFTWAREPRO A:41 , LYS A:42 , THR A:45 , SER A:48 , ARG A:123 , HOH A:396BINDING SITE FOR RESIDUE FMT A 411
05AC5SOFTWAREALA A:10 , HOH A:201 , FMT A:413BINDING SITE FOR RESIDUE FMT A 412
06AC6SOFTWAREPRO A:9 , ALA A:10 , HOH A:240 , FMT A:412BINDING SITE FOR RESIDUE FMT A 413
07AC7SOFTWAREALA A:137 , HOH A:174 , HOH A:220 , HOH A:244 , HOH A:288 , HOH A:366BINDING SITE FOR RESIDUE FMT A 414
08AC8SOFTWARESER A:76 , HOH A:165 , HOH A:297 , HOH A:394 , FMT A:410BINDING SITE FOR RESIDUE FMT A 415
09AC9SOFTWARELEU A:6 , GLU A:7 , HOH A:320 , HOH A:331BINDING SITE FOR RESIDUE FMT A 416
10BC1SOFTWARESER A:20 , PRO A:92 , HOH A:233 , HOH A:393BINDING SITE FOR RESIDUE FMT A 417
11BC2SOFTWAREALA A:29 , HIS A:33 , HOH A:276BINDING SITE FOR RESIDUE FMT A 418
12BC3SOFTWAREGLU A:99 , LEU A:119 , GLY A:120 , HOH A:401BINDING SITE FOR RESIDUE FMT A 419

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GKM)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GKM)

(-) Exons   (0, 0)

(no "Exon" information available for 3GKM)

(-) 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
 aligned with Q8P9V9_XANCP | Q8P9V9 from UniProtKB/TrEMBL  Length:160

    Alignment length:157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       
         Q8P9V9_XANCP     3 DAVLELPAATFDLPLSLSGGTQTTLRAHAGHWLVIYFYPKDSTPGCTTEGLDFNALLPEFDKAGAKILGVSRDSVKSHDNFCAKQGFAFPLVSDGDEALCRAFDVIKEKNMYGKQVLGIERSTFLLSPEGQVVQAWRKVKVAGHADAVLAALKAHAK 159
               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
                 3gkm A   3 DAVLELPAATFDLPLSLSGGTQTTLRAHAGHWLVIYFYPKDSTPGSTTEGLDFNALLPEFDKAGAKILGVSRDSVKSHDNFSAKQGFAFPLVSDGDEALCRAFDVIKEKNMYGKQVLGIERSTFLLSPEGQVVQAWRKVKVAGHADAVLAALKAHAK 159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152
   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 3GKM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8P9V9_XANCP | Q8P9V9)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    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.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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.

 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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3gkm)
 

(-) 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
  3gkm
    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)
  1.11.1.15
    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 3gkn 5im9 5ima 5imc 5imd 5imf 5imv 5imz 5iny 5io0 5io2 5iow 5iox 5ipg 5iph

(-) Related Entries Specified in the PDB File

3gkk 3gkn