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 THE CONSERVED HYPOTHETICAL PROTEIN TT1751 FROM THERMUS THERMOPHILUS HB8
 
Authors :  S. Kishishita, T. Terada, M. Shirouzu, S. Kuramitsu, S. -Y. Park, R. H. Tame, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  05 Feb 03  (Deposition) - 18 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  X-Ray Crystallography, Hypothetical, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kishishita, A. Tatsuguchi, R. Ushikoshi-Nakayama, T. Terada, S. Kuramitsu, S. -Y. Park, J. R. Tame, M. Shirouzu, S. Yokoyama
Crystal Structure Of A Conserved Hypothetical Protein Tt1751 From Thermus Thermophilus Hb8
Proteins V. 57 883 2004
PubMed-ID: 15481054  |  Reference-DOI: 10.1002/PROT.20282
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THE CONSERVED HYPOTHETICAL PROTEIN TT1751
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO31Ligand/IonSULFITE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:58 , ARG A:121 , ASN B:258 , ARG B:321BINDING SITE FOR RESIDUE SO3 A 3016

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J3M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:76 -Pro A:77
2Leu B:276 -Pro B:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J3M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J3M)

(-) Exons   (0, 0)

(no "Exon" information available for 1J3M)

(-) 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:127
 aligned with Q84BQ8_THETH | Q84BQ8 from UniProtKB/TrEMBL  Length:129

    Alignment length:127
                                    12        22        32        42        52        62        72        82        92       102       112       122       
         Q84BQ8_THETH     3 GMRKTLKATLAEARAQVEAALKEEGFGILTEIDVAATLKAKLGLEKPPYLILGACNPNLAARALEALPEIGLLLPCNVVLREAEEGVEVLIQDPKEMFRVLPEATQRALAPVAEEARTRLSRALSRL 129
               SCOP domains d1j3ma_ A: Hypothetical protein TT1751 (TTHA1732)                                                                               SCOP domains
               CATH domains 1j3mA00 A:3-129 TT1751-like                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3m A   3 GMRKTLKATLAEARAQVEAALKEEGFGILTEIDVAATLKAKLGLEKPPYLILGACNPNLAARALEALPEIGLLLPCNVVLREAEEGVEVLIQDPKEMFRVLPEATQRALAPVAEEARTRLSRALSRL 129
                                    12        22        32        42        52        62        72        82        92       102       112       122       


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with Q84BQ8_THETH | Q84BQ8 from UniProtKB/TrEMBL  Length:129

    Alignment length:127
                                    12        22        32        42        52        62        72        82        92       102       112       122       
         Q84BQ8_THETH     3 GMRKTLKATLAEARAQVEAALKEEGFGILTEIDVAATLKAKLGLEKPPYLILGACNPNLAARALEALPEIGLLLPCNVVLREAEEGVEVLIQDPKEMFRVLPEATQRALAPVAEEARTRLSRALSRL 129
               SCOP domains d1j3mb_ B: Hypothetical protein TT1751 (TTHA1732)                                                                               SCOP domains
               CATH domains 1j3mB00 B:203-329 TT1751-like                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3m B 203 GMRKTLKATLAEARAQVEAALKEEGFGILTEIDVAATLKAKLGLEKPPYLILGACNPNLAARALEALPEIGLLLPCNVVLREAEEGVEVLIQDPKEMFRVLPEATQRALAPVAEEARTRLSRALSRL 329
                                   212       222       232       242       252       262       272       282       292       302       312       322
   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J3M)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1J3M)

 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
    SO3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:76 - Pro A:77   [ RasMol ]  
    Leu B:276 - Pro B:277   [ RasMol ]  
 

(-) 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
  1j3m
    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
  Q84BQ8_THETH | Q84BQ8
    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
  Q84BQ8_THETH | Q84BQ8
    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 1J3M)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1J3M)