Structure of PDB 1psd Chain B Binding Site BS01

Receptor Information
>1psd Chain B (length=404) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHF
IGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPF
SNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGI
IGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDV
VSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASK
HLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENIGL
EVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLMHIHENRPGVLTALNK
IFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRA
RLLY
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 chain1psd Chain B Residue 450 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1psd The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase.
Resolution2.75 Å
Binding residue
(original residue number in PDB)		G158 Y159 G160 H161 I162 Y180 D181 I182 K185 H210 V211 P212 A238 S239 R240 H292
Binding residue
(residue number reindexed from 1)		G152 Y153 G154 H155 I156 Y174 D175 I176 K179 H204 V205 P206 A232 S233 R234 H286
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) N108 R240 D264 E269 H292
Catalytic site (residue number reindexed from 1) N102 R234 D258 E263 H286
Enzyme Commision number 1.1.1.399: 2-oxoglutarate reductase.
1.1.1.95: phosphoglycerate dehydrogenase.
Gene Ontology
Molecular Function
GO:0004617 phosphoglycerate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
GO:0047545 2-hydroxyglutarate dehydrogenase activity
GO:0051287 NAD binding
GO:0070403 NAD+ binding
GO:0070404 NADH binding
GO:0070905 serine binding
Biological Process
GO:0006564 L-serine biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1psd, PDBe:1psd, PDBj:1psd
PDBsum1psd
PubMed7719856
UniProtP0A9T0|SERA_ECOLI D-3-phosphoglycerate dehydrogenase (Gene Name=serA)

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