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 A HYPOTHETICAL PROTEIN TT1821 FROM THERMUS THERMOPHILUS
 
Authors :  Ihsanawati, T. Kaminishi, K. Murayama, T. Terada, M. Shirouzu, S. Yoko Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 Mar 05  (Deposition) - 17 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hypothetical Protein, Thermus Thermophilus, Structural Genomics, Nppsfa, Riken Structural Genomics/Proteomics Initiative, Rsgi, National Project On Protein Structural And Functional Analyses, Hydrolase, Nppsfa, National Project On Protein Structural And Functional Analyses (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Ihsanawati, T. Kaminishi, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structure Of A Hypothetical Protein Tt1821 From Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE THIOESTERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:8 , HOH B:526 , HOH B:585 , HOH B:586 , THR C:5BINDING SITE FOR RESIDUE GOL B 501
2AC2SOFTWAREGLU A:30 , ARG A:33 , TYR A:44 , PHE A:54 , PRO A:55 , HOH A:572 , HOH A:600 , MET C:17 , TYR D:11BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWAREGLU C:2 , HIS D:45 , ARG D:46BINDING SITE FOR RESIDUE GOL C 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z54)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z54)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z54)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z54)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z54)

(-) 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:132
 aligned with Q5SJV0_THET8 | Q5SJV0 from UniProtKB/TrEMBL  Length:132

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
         Q5SJV0_THET8     1 MESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIPEDIYRALSVLHLK 132
               SCOP domains d1z54a1 A:1-132 Probable thioesterase TTHA0908                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.hhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhh..ee..eeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeee.ee.......hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z54 A   1 MESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIPEDIYRALSVLHLK 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with Q5SJV0_THET8 | Q5SJV0 from UniProtKB/TrEMBL  Length:132

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
         Q5SJV0_THET8     1 MESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIPEDIYRALSVLHLK 132
               SCOP domains d1z54b_ B: Probable thioesterase TTHA0908                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.hhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhh.....eeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeee...-......hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1z54 B   1 MESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQV-ERAARIPEDIYRALSVLHLK 132
                                    10        20        30        40        50        60        70        80        90       100       110| |    120       130  
                                                                                                                                        111 |                   
                                                                                                                                          113                   


Chain C from PDB  Type:PROTEIN  Length:129
 aligned with Q5SJV0_THET8 | Q5SJV0 from UniProtKB/TrEMBL  Length:132

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
         Q5SJV0_THET8     2 ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIPEDIYRALSVLH 130
               SCOP domains d1z54c_ C: Probable thioesterase TTHA0908                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhh.ee..eeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeee.ee..ee...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z54 C   2 ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIPEDIYRALSVLH 130
                                    11        21        31        41        51        61        71        81        91       101       111       121         


Chain D from PDB  Type:PROTEIN  Length:130
 aligned with Q5SJV0_THET8 | Q5SJV0 from UniProtKB/TrEMBL  Length:132

    Alignment length:130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
         Q5SJV0_THET8     1 MESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIPEDIYRALSVLH 130
               SCOP domains d1z54d_ D: Probable thioesterase TTHA0908                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------4HBT-1z54D01 D:17-102                                                                 ---------------------------- Pfam domains (1)
           Pfam domains (2) ----------------4HBT-1z54D02 D:17-102                                                                 ---------------------------- Pfam domains (2)
           Pfam domains (3) ----------------4HBT-1z54D03 D:17-102                                                                 ---------------------------- Pfam domains (3)
           Pfam domains (4) ----------------4HBT-1z54D04 D:17-102                                                                 ---------------------------- Pfam domains (4)
         Sec.struct. author ..eeeeee.hhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhh.ee..eeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeeeee..eee..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z54 D   1 MESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIPEDIYRALSVLH 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z54)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: HotDog (52)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SJV0_THET8 | Q5SJV0)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1z54)
 

(-) 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
  1z54
    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
  Q5SJV0_THET8 | Q5SJV0
    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
  Q5SJV0_THET8 | Q5SJV0
    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 1Z54)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Z54)