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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE THIAMINE TRIPHOSPHATASE IN COMPLEX WITH THIAMINE TRIPHOSPHATE.
 
Authors :  J. Martinez, V. Truffault, M. Hothorn
Date :  24 Jun 15  (Deposition) - 05 Aug 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Triphosphate Tunnel Metalloenzyme, Thiamine Triphosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Martinez, V. Truffault, M. Hothorn
Structural Determinants For Substrate Binding And Catalysis In Triphosphate Tunnel Metalloenzymes.
J. Biol. Chem. V. 290 23348 2015
PubMed-ID: 26221030  |  Reference-DOI: 10.1074/JBC.M115.674473

(-) Compounds

Molecule 1 - THIAMINE TRIPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: THTPASE, THIAMINE TRIPHOSPHATASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2PGE2Ligand/IonTRIETHYLENE GLYCOL
3V4E2Ligand/IonTHIAMINE TRIPHOSPHATE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2PGE2Ligand/IonTRIETHYLENE GLYCOL
3V4E1Ligand/IonTHIAMINE TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2PGE-1Ligand/IonTRIETHYLENE GLYCOL
3V4E1Ligand/IonTHIAMINE TRIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:9 , LYS A:11 , TYR A:39 , ASP A:51 , TRP A:53 , ARG A:55 , ARG A:57 , LYS A:65 , TYR A:79 , ARG A:125 , GLU A:157 , GLU A:159 , ALA A:192 , LYS A:193 , HOH A:2001 , HOH A:2002 , HOH A:2006 , HOH A:2023 , HOH A:2038 , HOH A:2064 , HOH A:2075 , HOH A:2076 , HOH A:2077BINDING SITE FOR RESIDUE V4E A1000
2AC2SOFTWAREGLU B:9 , LYS B:11 , TYR B:39 , ASP B:51 , TRP B:53 , ARG B:55 , ARG B:57 , LYS B:65 , ASN B:77 , TYR B:79 , ARG B:125 , GLU B:157 , GLU B:159 , ALA B:192 , LYS B:193 , HOH B:2001 , HOH B:2003 , HOH B:2011 , HOH B:2012 , HOH B:2017BINDING SITE FOR RESIDUE V4E B1000
3AC3SOFTWARETHR A:124 , SER A:148 , ASP A:150 , EDO A:1219 , GLU B:117BINDING SITE FOR RESIDUE EDO A1216
4AC4SOFTWARESER A:60 , GLY A:61 , TRP A:62 , THR A:83 , GLU A:85 , HOH A:2088BINDING SITE FOR RESIDUE EDO A1217
5AC5SOFTWAREGLU A:58 , GLY A:59 , SER A:60BINDING SITE FOR RESIDUE EDO A1218
6AC6SOFTWAREASP A:150 , EDO A:1216 , SER B:120BINDING SITE FOR RESIDUE EDO A1219
7AC7SOFTWARETHR A:38 , GLU A:117 , SER A:120 , PRO A:203 , LEU A:204 , GLN A:207 , PGE A:1221 , HOH A:2089 , HOH A:2090 , HOH B:2042BINDING SITE FOR RESIDUE PGE A1220
8AC8SOFTWAREARG A:36 , ASP A:37 , THR A:38 , GLN A:56 , GLU A:58 , PGE A:1220 , HOH A:2090 , ARG B:36 , ILE B:122 , ASP B:150 , HOH B:2010 , HOH B:2042BINDING SITE FOR RESIDUE PGE A1221

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A64)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A64)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A64)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A64)

(-) Exons   (0, 0)

(no "Exon" information available for 5A64)

(-) 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:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhh..eeeeeeeeeeeeee...hhhhhh..eeeee...eeeeeee........eeeeeee.hhhhhhhhhhhhhh.......hhhhhh.....eeeeeeeeeeeeeee..eeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a64 A   4 GLIEVERKFAPGPDTEERLQELGATLEHRVTFRDTYYDTSELSLMLSDHWLRQREGSGWELKCPGVTGVSGPHNEYVEVTSEAAIVAQLFELLGSGEQKPAGVAAVLGSLKLQEVASFITTRSSWKLAQLTIDLDSADFGYAVGEVEAMVHEKAEVPAALEKIITVSSMLGVPAQEEAPAKLMVYLQRFRPLDYQRLLEAASS 215
                                    13        23        33        43        53        63        73        83        93       103       113       123       142       152       162       172       182       192       202       212   
                                                                                                                                                         131|                                                                          
                                                                                                                                                          141                                                                          


Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhh..eeeeeeeeeeeeee...hhhhhh..eeeee...eeeeee..eeeeee.hhhhhhhhhhhhhh.......hhhhhh.....eeeeeeeeeeeeeee..eeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a64 B   4 GLIEVERKFAPGPDTEERLQELGATLEHRVTFRDTYYDTSELSLMLSDHWLRQREGSGWELKCPHNEYVEVTSEAAIVAQLFELLGSGEQKPAGVAAVLGSLKLQEVASFITTRSSWKLAQLTIDLDSADFGYAVGEVEAMVHEKAEVPAALEKIITVSSMLGVPAQEEAPAKLMVYLQRFRPLDYQRLLEA 212
                                    13        23        33        43        53        63   ||   81        91       101       111       121       131|      150       160       170       180       190       200       210  
                                                                                          67|                                                    131|                                                                       
                                                                                           76                                                     141
   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 5A64)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A64)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A64)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    V4E  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5a64)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  5a64
    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
  THTPA_MOUSE | Q8JZL3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.1.28
    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
  THTPA_MOUSE | Q8JZL3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        THTPA_MOUSE | Q8JZL3: 2jmu 5a65

(-) Related Entries Specified in the PDB File

5a5y CRYSTAL STRUCTURE OF ATTTM3 IN COMPLEX WITH TRIPOLYPHOSPHATE AND MAGNESIUM ION (FORM A)
5a60 CRYSTAL STRUCTURE OF FULL-LENGTH E. COLI YGIF IN COMPLEX WITH TRIPOLYPHOSPHATE AND TWO MAGNESIUM IONS
5a61 CRYSTAL STRUCTURE OF FULL-LENGTH E. COLI YGIF IN COMPLEX WITH TRIPOLYPHOSPHATE AND TWO MANGANESE IONS.
5a65 CRYSTAL STRUCTURE OF MOUSE THIAMINE TRIPHOSPHATASE IN COMPLEX WITH THIAMINE DIPHOSPHATE, ORTHOPHOSPHATE AND MAGNESIUM IONS.
5a66 CRYSTAL STRUCTURE OF ATTTM3 IN COMPLEX WITH TRIPOLYPHOSPHATE AND MANGANESE ION (FORM A)
5a67 CRYSTAL STRUCTURE OF ATTTM3 IN COMPLEX WITH TRIPOLYPHOSPHATE AND MANGANESE ION (FORM B)
5a68 CRYSTAL STRUCTURE OF THE ATTTM3 PRODUCT COMPLEX WITH TWO ORTHOPHOSPHATES AND MANGANESE IONS (FORM B)