Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF TT1380 PROTEIN FROM THERMUS THERMOPHILUS
 
Authors :  T. Wada, M. Shirouzu, S. -Y. Park, J. R. H. Tame, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  05 Mar 02  (Deposition) - 09 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Wada, M. Shirouzu, T. Terada, Y. Kamewari, S. -Y. Park, J. R. H. Tame, S. Kuramitsu, S. Yokoyama
Crystal Structure Of The Conserved Hypothetical Protein Tt1380 From Thermus Thermophilus Hb8
Proteins V. 55 778 2004
PubMed-ID: 15103643  |  Reference-DOI: 10.1002/PROT.20122
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TT1380
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1ZN7Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:16 , GLU A:60 , GLU B:67 , ZN B:2002BINDING SITE FOR RESIDUE ZN B 2001
2AC2SOFTWAREGLU A:60 , GLU B:60 , HOH B:1027 , ZN B:2001 , ZN B:2003 , ZN B:2005BINDING SITE FOR RESIDUE ZN B 2002
3AC3SOFTWAREGLU A:67 , GLU B:60 , ARG B:63 , ZN B:2002 , ZN B:2004 , ZN B:2005BINDING SITE FOR RESIDUE ZN B 2003
4AC4SOFTWAREARG B:63 , ZN B:2003 , ZN B:2005BINDING SITE FOR RESIDUE ZN B 2004
5AC5SOFTWAREZN B:2002 , ZN B:2003 , ZN B:2004BINDING SITE FOR RESIDUE ZN B 2005
6AC6SOFTWAREHIS B:75 , HOH B:1046BINDING SITE FOR RESIDUE ZN B 2006
7AC7SOFTWAREARG A:25 , HIS A:75 , HOH A:1001 , HOH A:1017BINDING SITE FOR RESIDUE ZN A 2007

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IUJ)

(-) Sequences/Alignments

Asymmetric 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:102
 aligned with P83693_THETH | P83693 from UniProtKB/TrEMBL  Length:106

    Alignment length:102
                                    10        20        30        40        50        60        70        80        90       100  
         P83693_THETH     1 MFVTMNRIPVRPEYAEQFEEAFRQRARLVDRMPGFIRNLVLRPKNPGDPYVVMTLWESEEAFRAWTESPAFKEGHARSGTLPKEAFLGPNRLEAFEVVLDSE 102
               SCOP domains d1iuja_ A: Hypothetical protein TT1380                                                                 SCOP domains
               CATH domains 1iujA00 A:1-102  [code=3.30.70.900, no name defined]                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhh...............eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1iuj A   1 MFVTMNRIPVRPEYAEQFEEAFRQRARLVDRMPGFIRNLVLRPKNPGDPYVVMTLWESEEAFRAWTESPAFKEGHARSGTLPKEAFLGPNRLEAFEVVLDSE 102
                                    10        20        30        40        50        60        70        80        90       100  


Chain B from PDB  Type:PROTEIN  Length:103
 aligned with P83693_THETH | P83693 from UniProtKB/TrEMBL  Length:106

    Alignment length:103
                                    10        20        30        40        50        60        70        80        90       100   
         P83693_THETH     1 MFVTMNRIPVRPEYAEQFEEAFRQRARLVDRMPGFIRNLVLRPKNPGDPYVVMTLWESEEAFRAWTESPAFKEGHARSGTLPKEAFLGPNRLEAFEVVLDSEG 103
               SCOP domains d1iujb_ B: Hypothetical protein TT1380                                                                  SCOP domains
               CATH domains 1iujB00 B:1-103  [code=3.30.70.900, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhh......hhhhh....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1iuj B   1 MFVTMNRIPVRPEYAEQFEEAFRQRARLVDRMPGFIRNLVLRPKNPGDPYVVMTLWESEEAFRAWTESPAFKEGHARSGTLPKEAFLGPNRLEAFEVVLDSEG 103
                                    10        20        30        40        50        60        70        80        90       100
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 Visualization

(-) Interactive Views

Asymmetric 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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1iuj)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  1iuj
    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
  P83693_THETH | P83693
    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
  P83693_THETH | P83693
    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 1IUJ)

(-) Related Entries Specified in the PDB File

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