Structure of PDB 1yba Chain C Binding Site BS02

Receptor Information
>1yba Chain C (length=406) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDA
HFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNA
PFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKL
GIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMS
DVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALA
SKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENI
GLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLMHIHENRPGVLTAL
NKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTI
RARLLY
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 chain1yba Chain C Residue 415 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1yba Vmax Regulation through Domain and Subunit Changes. The Active Form of Phosphoglycerate Dehydrogenase
Resolution2.24 Å
Binding residue
(original residue number in PDB)		I84 F106 G160 H161 I162 Y180 D181 I182 K185 H210 V211 P212 A238 S239 R240 G294
Binding residue
(residue number reindexed from 1)		I80 F102 G156 H157 I158 Y176 D177 I178 K181 H206 V207 P208 A234 S235 R236 G290
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) N108 R240 D264 E269 H292
Catalytic site (residue number reindexed from 1) N104 R236 D260 E265 H288
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1yba, PDBe:1yba, PDBj:1yba
PDBsum1yba
PubMed15823035
UniProtP0A9T0|SERA_ECOLI D-3-phosphoglycerate dehydrogenase (Gene Name=serA)

[Back to BioLiP]