Structure of PDB 1yba Chain B Binding Site BS01

Receptor Information
>1yba Chain B (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 IDAKG
InChIInChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
InChIKeyKPGXRSRHYNQIFN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(=O)CCC(=O)O
OpenEye OEToolkits 1.7.6C(CC(=O)O)C(=O)C(=O)O
CACTVS 3.385OC(=O)CCC(=O)C(O)=O
FormulaC5 H6 O5
Name2-OXOGLUTARIC ACID
ChEMBLCHEMBL1686
DrugBankDB08845
ZINCZINC000001532519
PDB chain1yba Chain B Residue 412 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1yba Vmax Regulation through Domain and Subunit Changes. The Active Form of Phosphoglycerate Dehydrogenase
Resolution2.24 Å
Binding residue
(original residue number in PDB)		S61 C83
Binding residue
(residue number reindexed from 1)		S57 C79
Annotation score5
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

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

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