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 AN ORGANIC HYDROPEROXIDE RESISTANCE PROTEIN FROM BURKHOLDERIA CENOCEPACIA
 
Authors :  D. M. Dranow, C. M. Lukacs, T. E. Edwards, D. Lorimer, Seattle Structur Genomics Center For Infectious Disease (Ssgcid)
Date :  20 Nov 13  (Deposition) - 04 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Osmc-Like Protein, Organic Hydroperoxide Resistance, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Dranow, C. M. Lukacs, T. E. Edwards, D. Lorimer
Crystal Structure Of An Organic Hydroperoxide Resistance Protein From Burkholderia Cenocepacia
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ORGANIC HYDROPEROXIDE RESISTANCE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: OHR, BCEJ2315_63600, BCAS0085
    Organism Scientific: BURKHOLDERIA CENOCEPACIA
    Organism Taxid: 216591
    Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:31 , ALA A:47 , HOH A:508 , SER B:27 , LEU B:29 , HOH B:393BINDING SITE FOR RESIDUE EDO A 301
2AC2SOFTWAREVAL A:6 , ARG A:9 , HOH A:408BINDING SITE FOR RESIDUE EDO A 302
3AC3SOFTWAREHOH A:512BINDING SITE FOR RESIDUE EDO A 303
4AC4SOFTWAREASP A:72 , ARG A:119 , HOH A:436BINDING SITE FOR RESIDUE EDO A 304
5AC5SOFTWAREHOH A:443 , HOH A:466 , HOH A:507BINDING SITE FOR RESIDUE EDO A 305
6AC6SOFTWAREILE A:91 , PRO A:92 , HOH A:448 , MET B:1 , ASN B:128 , HOH B:372BINDING SITE FOR RESIDUE EDO A 306
7AC7SOFTWAREASP A:118 , ARG A:131 , PRO B:92 , ASN B:93 , HOH B:354 , HOH B:424BINDING SITE FOR RESIDUE EDO B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NOZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NOZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NOZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NOZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4NOZ)

(-) 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:142
                                                                                                                                                                              
               SCOP domains d4noza_ A: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeee.....eee......eee...hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4noz A   0 HMSIEKVLYRAHAKATGGRDGRATVPESGLDLKLTTPRELGGAGGAGANPEQLFAAGYSACFIGAMKFVAARDKIAIPADAAIEGSVGIGAIPNGFGIEVELKISLPGLDRDIAQTLIDRAHVVCPYSNATRGNIDVTLTLV 141
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139  


Chain B from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains d4nozb_ B: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee.....eeee....eeee...hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4noz B  -6 AHHHHHHMSIEKVLYRAHAKATGGRDGRATVPESGLDLKLTTPRELGGAGGAGANPEQLFAAGYSACFIGAMKFVAARDKIAIPADAAIEGSVGIGAIPNGFGIEVELKISLPGLDRDIAQTLIDRAHVVCPYSNATRGNIDVTLTLV 141
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NOZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NOZ)

(-) Gene Ontology  (1, 1)

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
    EDO  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4noz)
 

(-) 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
  4noz
    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
  B4EPK2_BURCJ | B4EPK2
    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
  B4EPK2_BURCJ | B4EPK2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4NOZ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4NOZ)