Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TTK003001694 FROM THERMUS THERMOPHILUS HB8
 
Authors :  H. Wang, K. Murayama, T. Terada, M. Shirouzu, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  12 Jan 05  (Deposition) - 12 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Unknown Function, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wang, K. Murayama, T. Terada, M. Shirouzu, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Ttk003001694 From Thermus Thermophilus Hb8
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TTHA0636
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS HB8
    Organism Taxid: 300852
    Strain: HB8 / ATCC 27634 / DSM 579

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1WWP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WWP)

(-) 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:119
 aligned with Q5SKK7_THET8 | Q5SKK7 from UniProtKB/TrEMBL  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         Q5SKK7_THET8     1 MAEKALATLKELAFLEDPSPVERDAAIQRFEYTFEAFWKALQAYLREKEGLEGASPKGVIRLAREVGLLRDEEARLALGMVDDRSLTVHTYNEPLARAIFRRLPDYARLMEQVLGRLRR 119
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1wwp A   1 mAEKALATLKELAFLEDPSPVERDAAIQRFEYTFEAFWKALQAYLREKEGLEGASPKGVIRLAREVGLLRDEEARLALGmVDDRSLTVHTYNEPLARAIFRRLPDYARLmEQVLGRLRR 119
                            |       10        20        30        40        50        60        70        80        90       100       110         
                            |                                                                             80-MSE                       110-MSE     
                            1-MSE                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with Q5SKK7_THET8 | Q5SKK7 from UniProtKB/TrEMBL  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         Q5SKK7_THET8     1 MAEKALATLKELAFLEDPSPVERDAAIQRFEYTFEAFWKALQAYLREKEGLEGASPKGVIRLAREVGLLRDEEARLALGMVDDRSLTVHTYNEPLARAIFRRLPDYARLMEQVLGRLRR 119
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) NTase_sub_bind-1wwpB01 B:1-119                                                                                          Pfam domains (1)
           Pfam domains (2) NTase_sub_bind-1wwpB02 B:1-119                                                                                          Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1wwp B   1 mAEKALATLKELAFLEDPSPVERDAAIQRFEYTFEAFWKALQAYLREKEGLEGASPKGVIRLAREVGLLRDEEARLALGmVDDRSLTVHTYNEPLARAIFRRLPDYARLmEQVLGRLRR 119
                            |       10        20        30        40        50        60        70        80        90       100       110         
                            1-MSE                                                                         80-MSE                       110-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  (0, 0)

(no "SCOP Domain" information available for 1WWP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WWP)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: KNTase_C (11)

(-) Gene Ontology  (0, 0)

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

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

(-) 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 ](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
  1wwp
    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
  Q5SKK7_THET8 | Q5SKK7
    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
  Q5SKK7_THET8 | Q5SKK7
    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 1WWP)

(-) Related Entries Specified in the PDB File

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