Structure of PDB 2d8a Chain A Binding Site BS03

Receptor Information
>2d8a Chain A (length=333) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKMVAIMKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWN
EWAQSRIKPPQIMGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYT
KIFGVDTDGVFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDTVLAG
PISGKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGAD
YVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVS
LLGLYPGKVTIDFNNLIIFKALTIYGITGRHLWETWYTVSRLLQSGKLNL
DPIITHKYKGFDKYEEAFELMRAGKTGKVVFML
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain2d8a Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2d8a Crystal Structure of PH0655 from Pyrococcus horikoshii OT3
Resolution2.05 Å
Binding residue
(original residue number in PDB)		G175 G177 P178 L179 S198 E199 P200 R204 F243 S244 A246 L266 G267 L268 T292
Binding residue
(residue number reindexed from 1)		G161 G163 P164 L165 S184 E185 P186 R190 F229 S230 A232 L252 G253 L254 T278
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) C42 G43 T44 H47 H67 E68 C97 C100 K115 P153 A157 K342
Catalytic site (residue number reindexed from 1) C40 G41 T42 H45 H65 E66 C95 C98 K101 P139 A143 K328
Enzyme Commision number 1.1.1.103: L-threonine 3-dehydrogenase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0008743 L-threonine 3-dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016597 amino acid binding
GO:0030554 adenyl nucleotide binding
GO:0043168 anion binding
GO:0046872 metal ion binding
GO:0070401 NADP+ binding
GO:0070403 NAD+ binding
Biological Process
GO:0006566 threonine metabolic process
GO:0006567 threonine catabolic process
GO:0019518 L-threonine catabolic process to glycine
GO:0051262 protein tetramerization
GO:0051289 protein homotetramerization
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2d8a, PDBe:2d8a, PDBj:2d8a
PDBsum2d8a
PubMed
UniProtO58389|TDH_PYRHO L-threonine 3-dehydrogenase (Gene Name=tdh)

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