Structure of PDB 3gfb Chain D Binding Site BS01

Receptor Information
>3gfb Chain D (length=347) Species: 69014 (Thermococcus kodakarensis KOD1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKMQAIMKTKPAYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWN
EWAQSRIKPPQIMGHEVAGEVVEVGPGVEDLQVGDYISVETHIVCGKCYA
CKHNRYHVCQNTKIFGVDMDGVFAHYAIVPAKNAWKNPKDMPPEYAALQE
PLGNAVDTVLAGPIAGRSTLITGAGPLGLLGIAVAKASGAYPVIVSEPSE
FRRKLAKKVGADYVVNPFEEDPVKFVMDITDGAGVEVFLEFSGAPKALEQ
GLKAVTPGGRVSLLGLFPREVTIDFNNLIIFKALEVHGITGRHLWETWYT
VSSLIQSGKLNLDPIITHKYKGFDKFEEAFELMRAGKTGKVVFFPHK
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 chain3gfb Chain D Residue 503 [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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PDB3gfb Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G177 P178 L179 S198 E199 P200 R204 F243 S244 A246 L266 G267 L268 I291 T292
Binding residue
(residue number reindexed from 1)		G175 P176 L177 S196 E197 P198 R202 F241 S242 A244 L264 G265 L266 I289 T290
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) C42 G43 T44 H47 H67 E68 C97 C100 C103 C111 K115 P153 A157 K342
Catalytic site (residue number reindexed from 1) C40 G41 T42 H45 H65 E66 C95 C98 C101 C109 K113 P151 A155 K340
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: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:3gfb, PDBe:3gfb, PDBj:3gfb
PDBsum3gfb
PubMed19616102
UniProtQ5JI69|TDH_THEKO L-threonine 3-dehydrogenase (Gene Name=tdh)

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