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(-) Description

Title :  STRUCTURE OF TT0495 PROTEIN FROM THERMUS THERMOPHILUS
 
Authors :  N. K. Lokanath, K. J. Pampa, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  23 Mar 07  (Deposition) - 01 Apr 08  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (2x)
Keywords :  Gluconate Dehydrogenase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Pampa, N. K. Lokanath, N. Kunishima, R. V. Rai
The First Crystal Structure Of Nad-Dependent 3-Dehydro-2-Deoxy-D-Gluconate Dehydrogenase From Thermus Thermophilus Hb8
Acta Crystallogr. , Sect. D V. 70 994 2014
PubMed-ID: 24699644  |  Reference-DOI: 10.1107/S1399004713034925

(-) Compounds

Molecule 1 - 2-DEOXY-D-GLUCONATE 3-DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.125
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: GLUCONATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A
Biological Unit 2 (2x): A
Biological Unit 3 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:9 , SER A:11 , ARG A:12 , GLY A:13 , ILE A:14 , SER A:33 , THR A:50 , ASP A:51 , LEU A:52 , GLU A:53 , ALA A:77 , ALA A:78 , ALA A:79 , HIS A:101 , GLU A:118 , ILE A:127 , GLY A:128 , TYR A:144 , LYS A:148 , PRO A:174 , GLY A:175 , THR A:179 , PHE A:181 , THR A:182 , HOH A:1347 , HOH A:1353 , HOH A:1354 , HOH A:1415 , HOH A:1474 , HOH A:1475 , HOH A:1498 , HOH A:1554BINDING SITE FOR RESIDUE NAD A 1300
2AC2SOFTWAREASP A:56 , LYS A:58 , HOH A:1390 , HOH A:1424 , HOH A:1547 , HOH A:1632 , HOH A:1637BINDING SITE FOR RESIDUE GOL A 1301
3AC3SOFTWAREGLY A:70 , LEU A:71 , HIS A:72 , HIS A:115 , HOH A:1343 , HOH A:1634BINDING SITE FOR RESIDUE GOL A 1302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EKP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EKP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EKP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EKP)

(-) Exons   (0, 0)

(no "Exon" information available for 2EKP)

(-) 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:238
 aligned with Q53W82_THET8 | Q53W82 from UniProtKB/TrEMBL  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
         Q53W82_THET8     2 ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTDLEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLHLDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTALLGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPMGRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY 239
               SCOP domains d2ekpa_ A: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2ekpA00 A:2-239 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee..hhhhhhhhh.eeee......hhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ekp A   2 ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTDLEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLHLDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTALLGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPMGRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EKP)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q53W82_THET8 | Q53W82)
molecular function
    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.

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  2ekp
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  Q53W82_THET8 | Q53W82
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  1.1.1.125
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 Related Entries

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

UniProtKB/TrEMBL
        Q53W82_THET8 | Q53W82: 1x1e 2ekq 4jp2 4jp3

(-) Related Entries Specified in the PDB File

2ekq SECOND FORM OF THE SAME PROTEIN RELATED ID: TTK003000495.2 RELATED DB: TARGETDB