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 L-THREONINE DEHYDROGENASE FROM HYPERTHERMOPHILIC ARCHAEON THERMOPLASMA VOLCANIUM
 
Authors :  K. Yoneda, H. Sakuraba, T. Ohshima
Date :  18 Apr 09  (Deposition) - 31 Mar 10  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B
Keywords :  L-Threonine Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yoneda, H. Sakuraba, T. Araki, T. Ohshima
Crystal Structure Of Binary And Ternary Complexes Of Archaeal Udp-Galactose 4-Epimerase-Like L-Threonine Dehydrogenase From Thermoplasma Volcanium.
J. Biol. Chem. V. 287 12966 2012
PubMed-ID: 22374996  |  Reference-DOI: 10.1074/JBC.M111.336958

(-) Compounds

Molecule 1 - NDP-SUGAR EPIMERASE
    Chains: A, B
    EC Number: 1.1.1.103
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOPLASMA VOLCANIUM
    Organism Taxid: 50339
    Synonym: L-THREONINE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:8 , GLY A:9 , GLN A:10 , ILE A:11 , ASP A:32 , ILE A:33 , LEU A:46 , ASP A:47 , VAL A:48 , LEU A:69 , ALA A:70 , GLY A:71 , LEU A:73 , VAL A:87 , PRO A:110 , SER A:111 , TYR A:137 , LYS A:141 , TYR A:164 , HOH A:328 , HOH A:378 , HOH A:390BINDING SITE FOR RESIDUE NAD A 3001
2AC2SOFTWARESER B:8 , GLY B:9 , GLN B:10 , ILE B:11 , ASP B:32 , ILE B:33 , LEU B:46 , ASP B:47 , VAL B:48 , LEU B:69 , ALA B:70 , GLY B:71 , LEU B:73 , PRO B:110 , SER B:111 , TYR B:137 , LYS B:141 , TYR B:164 , HOH B:362 , HOH B:367 , HOH B:402 , HOH B:445BINDING SITE FOR RESIDUE NAD B 3002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A1N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A1N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A1N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A1N)

(-) Exons   (0, 0)

(no "Exon" information available for 3A1N)

(-) 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:315
 aligned with Q97BK3_THEVO | Q97BK3 from UniProtKB/TrEMBL  Length:317

    Alignment length:315
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     
         Q97BK3_THEVO     1 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEKLGIEGKH 315
               SCOP domains d3a1na_ A: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhhhhhh...eeeee.........eeee....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh..................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee...........hhhhhhhhhhhh...eee.......eeeeehhhhhhhhhhhhhhhhhhh.....ee...eeehhhhhhhhhhh......eee..hhhhhhhh.......hhhhhhhhh.....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1n A   1 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEKLGIEGKH 315
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with Q97BK3_THEVO | Q97BK3 from UniProtKB/TrEMBL  Length:317

    Alignment length:309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300         
         Q97BK3_THEVO     1 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEKL 309
               SCOP domains d3a1nb_ B: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhhhhhh...eeeee..........eee....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh..................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee...........hhhhhhhhhhhh..eeee.......eeeeehhhhhhhhhhhhhh........eeee...eeehhhhhhhhhhh.....eeee..hhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1n B   1 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEKL 309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A1N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A1N)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q97BK3_THEVO | Q97BK3)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 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
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3a1n)
 

(-) 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
  3a1n
    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
  Q97BK3_THEVO | Q97BK3
    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)
  1.1.1.103
    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
  Q97BK3_THEVO | Q97BK3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q97BK3_THEVO | Q97BK3: 3a4v 3a9w 3ajr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3A1N)