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 :  CRYSTAL STRUCTURE OF THE POLYISOPRENOID-BINDING PROTEIN, TT1927B, FROM THERMUS THERMOPHILUS HB8
 
Authors :  N. Handa, M. Idaka, T. Terada, H. Hamana, Y. Ishizuka, S. -Y. Park, J. R. H. Tame, Y. Doi-Katayama, H. Hirota, S. Kuramitsu, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  03 Dec 04  (Deposition) - 21 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Barrel, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Handa, T. Terada, Y. Doi-Katayama, H. Hirota, J. R. Tame, S. -Y. Park, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Crystal Structure Of A Novel Polyisoprenoid-Binding Protein From Thermus Thermophilus Hb8
Protein Sci. V. 14 1004 2005
PubMed-ID: 15741337  |  Reference-DOI: 10.1110/PS.041183305
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN TT1927B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: POLYISOPRENOID-BINDING PROTEIN TT1927B

 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
1OTP1Ligand/Ion(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYLTRIHYDROGEN DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , PHE A:14 , HIS A:18 , VAL A:24 , LEU A:28 , VAL A:46 , ALA A:48 , ARG A:62 , HIS A:65 , PHE A:82 , LYS A:121 , LEU A:144 , TRP A:146 , VAL A:157 , PHE A:163 , HOH A:1097BINDING SITE FOR RESIDUE OTP A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WUB)

(-) 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:176
 aligned with P83815_THETH | P83815 from UniProtKB/TrEMBL  Length:178

    Alignment length:176
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      
         P83815_THETH     1 MKWNLDPSHTSIDFKVRHMGIASVRGSLKVLSGSVETDEAGRPIQVEAVIDAASIATGEPQRDGHLRSADFLHAEQYPEIRFVSTQIEPLGGNRYRIQGNLTIRDITKPVTLEAEVSAPIKDPWGMQRVAASASGQINRKDWNLTWNQVLELGALLVGEEVKFNLEVEAVAPAPVA 176
               SCOP domains d1wuba_ A: Polyisoprenoid-binding protein TTHA0802 (TT1927B)                                                                                                                     SCOP domains
               CATH domains 1wubA00 A:1-176 Protein ycei                                                                                                                                                     CATH domains
               Pfam domains -YceI-1wubA01 A:2-170                                                                                                                                                     ------ Pfam domains
         Sec.struct. author .eeee.hhhheeeeeeee...eeeeeeeeeeeeeeee.....eeeeeeeeeeeeee..hhhhhhhhhh..........eeeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeee...ee.....eeeeeeeeeeee.hhhh................eeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wub A   1 MKWNLDPSHTSIDFKVRHMGIASVRGSLKVLSGSVETDEAGRPIQVEAVIDAASIATGEPQRDGHLRSADFLHAEQYPEIRFVSTQIEPLGGNRYRIQGNLTIRDITKPVTLEAEVSAPIKDPWGMQRVAASASGQINRKDWNLTWNQVLELGALLVGEEVKFNLEVEAVAPAPVA 176
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: YceI] (5)

(-) Gene Ontology  (0, 0)

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

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

(-) 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
  1wub
    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
  P83815_THETH | P83815
    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
  P83815_THETH | P83815
    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 1WUB)

(-) Related Entries Specified in the PDB File

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