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
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CONSERVED HYPOTHETICAL PROTEIN TT2028 FROM AN EXTREMELY THERMOPHILIC BACTERIUM THERMUS THERMOPHILUS HB8
 
Authors :  E. Mizohata, R. Ushikoshi-Nakayama, T. Terada, K. Murayama, H. Sakai, S. Kuramitsu, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  07 Jan 05  (Deposition) - 07 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tena/Thi-4 Family, Putative Transctiption Activator, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Mizohata, R. Ushikoshi-Nakayama, T. Terada, K. Murayama, H. Sakai S. Kuramitsu, M. Shirouzu, S. Yokoyama
Crystal Structure Of Tt2028 From An Extremely Thermophilic Bacterium Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TT2028
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1WWM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:12 -Pro A:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WWM)

(-) 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:180
 aligned with Q5SLX4_THET8 | Q5SLX4 from UniProtKB/TrEMBL  Length:188

    Alignment length:180
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
         Q5SLX4_THET8     9 EVPGLLEEIKALPLRLDEERFRFWLQQDYPFVEALYRYQVGLLLEAPQAHRAPLVQALMATVEELDWLLLQGASPSAPVHPVRAGYIALLEEMGRLPYAYRVVFFYFLNGLFLEAWAHHVPEEGPWAELSQHWFAPEFQAVLYDLEVLARGLWEDLDPEVVRTYLRRILEAEKATWSLLL 188
               SCOP domains d1wwma1 A:11-190 Hypothetical protein TTHA0169 (TT2028)                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wwm A  11 EVPGLLEEIKALPLRLDEERFRFWLQQDYPFVEALYRYQVGLLLEAPQAHRAPLVQALmATVEELDWLLLQGASPSAPVHPVRAGYIALLEEmGRLPYAYRVVFFYFLNGLFLEAWAHHVPEEGPWAELSQHWFAPEFQAVLYDLEVLARGLWEDLDPEVVRTYLRRILEAEKATWSLLL 190
                                    20        30        40        50        60        70        80        90       100  |    110       120       130       140       150       160       170       180       190
                                                                                     69-MSE                           103-MSE                                                                                   


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with Q5SLX4_THET8 | Q5SLX4 from UniProtKB/TrEMBL  Length:188

    Alignment length:178
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q5SLX4_THET8    11 PGLLEEIKALPLRLDEERFRFWLQQDYPFVEALYRYQVGLLLEAPQAHRAPLVQALMATVEELDWLLLQGASPSAPVHPVRAGYIALLEEMGRLPYAYRVVFFYFLNGLFLEAWAHHVPEEGPWAELSQHWFAPEFQAVLYDLEVLARGLWEDLDPEVVRTYLRRILEAEKATWSLLL 188
               SCOP domains d1wwmb_ B: automated matches                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh-----------------hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wwm B  13 PGLLEEIKALPLRLDEERFRFWLQQDYPFVEALYRYQVGLLLEAPQAHRAPLVQALmATVEELDWLLLQGASPSAPVHPVRAGYIALLEEmGRLPYAYRVVFFYFLNGLFLEAWAHHV-----------------FQAVLYDLEVLARGLWEDLDPEVVRTYLRRILEAEKATWSLLL 190
                                    22        32        42        52        62      | 72        82        92       102|      112       122       | -         -     | 152       162       172       182        
                                                                                   69-MSE                           103-MSE                    130               148
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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 1wwm)
 
  Cis Peptide Bonds
    Val A:12 - Pro A:13   [ 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 ](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
  1wwm
    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
  Q5SLX4_THET8 | Q5SLX4
    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
  Q5SLX4_THET8 | Q5SLX4
    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 1WWM)

(-) Related Entries Specified in the PDB File

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