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 :  YFFB (PA3664) PROTEIN
 
Authors :  A. Teplyakov, S. Pullalarevu, G. Obmolova, V. Doseeva, A. Galkin, O. He M. Dauter, Z. Dauter, G. L. Gilliland, Structure 2 Function Projec
Date :  15 Dec 03  (Deposition) - 02 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.02
Chains :  Asym./Biol. Unit :  A
Keywords :  Thioredoxin Fold, Structure 2 Function Project, S2F, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Teplyakov, S. Pullalarevu, G. Obmolova, V. Doseeva, A. Galkin, O. Herzberg, M. Dauter, Z. Dauter, G. L. Gilliland
Crystal Structure Of The Yffb Protein From Pseudomonas Aeruginosa Suggests A Glutathione-Dependent Thiol Reductase Function.
Bmc Struct. Biol. V. 4 5 2004
PubMed-ID: 15102337  |  Reference-DOI: 10.1186/1472-6807-4-5

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN YFFB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET100-D-TOPO
    Expression System Strain: B834 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YFFB
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:100BINDING SITE FOR RESIDUE IPA A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RW1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RW1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RW1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RW1)

(-) Exons   (0, 0)

(no "Exon" information available for 1RW1)

(-) 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:114
 aligned with Q9HXX5_PSEAE | Q9HXX5 from UniProtKB/TrEMBL  Length:115

    Alignment length:114
                                    11        21        31        41        51        61        71        81        91       101       111    
         Q9HXX5_PSEAE     2 TYVLYGIKACDTMKKARTWLDEHKVAYDFHDYKAVGIDREHLRRWCAEHGWQTVLNRAGTTFRKLDEAQKADLDEAKAIELMLAQPSMIKRPVLELGGRTLVGFKPDAYAAALA 115
               SCOP domains d1rw1a_ A: Hypothetical protein PA3664 (YffB)                                                                      SCOP domains
               CATH domains 1rw1A00 A:2-115 Glutaredoxin                                                                                       CATH domains
               Pfam domains ----ArsC-1rw1A01 A:6-113                                                                                        -- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh...eeeeehhhhh.hhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhh..hhhhhhhhhhhhhhhh...eee....eee..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1rw1 A   2 TYVLYGIKACDTmKKARTWLDEHKVAYDFHDYKAVGIDREHLRRWCAEHGWQTVLNRAGTTFRKLDEAQKADLDEAKAIELmLAQPSmIKRPVLELGGRTLVGFKPDAYAAALA 115
                                    11  |     21        31        41        51        61        71        81 |     |91       101       111    
                                       14-MSE                                                               83-MSE |                          
                                                                                                                  89-MSE
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1RW1)

 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
    IPA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1rw1)
 

(-) 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
  1rw1
    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
  Q9HXX5_PSEAE | Q9HXX5
    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
  Q9HXX5_PSEAE | Q9HXX5
    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 1RW1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RW1)