Structure of PDB 2p9e Chain D Binding Site BS01

Receptor Information
>2p9e Chain D (length=403) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFI
GLRSRTHLTEDVINAAEKLVAIGAFAIGTNQVDLDAAAKRGIPVFNAPFS
NTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGII
GYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVV
SLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALADALASKH
LAGAAIDVFPTEPATNSDPFTSPLAEFDNVLLTPHIGGSTQEAQENIGLE
VAGKLIKYSDNGSTLSAVNFPEVSLPLHVGRRLMHIHENRPGVLTALNKI
FAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRAR
LLY
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/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/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain2p9e Chain D Residue 511 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2p9e The Effect of Hinge Mutations on Effector Binding and Domain Rotation in Escherichia coli D-3-Phosphoglycerate Dehydrogenase
Resolution2.6 Å
Binding residue
(original residue number in PDB)		V112 G160 H161 I162 Y180 D181 I182 K185 H210 V211 P212 A238 S239 R240 H292 G294 G295
Binding residue
(residue number reindexed from 1)		V105 G153 H154 I155 Y173 D174 I175 K178 H203 V204 P205 A231 S232 R233 H285 G287 G288
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) N108 R240 D264 E269 H292
Catalytic site (residue number reindexed from 1) N101 R233 D257 E262 H285
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:2p9e, PDBe:2p9e, PDBj:2p9e
PDBsum2p9e
PubMed17459882
UniProtP0A9T0|SERA_ECOLI D-3-phosphoglycerate dehydrogenase (Gene Name=serA)

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