Structure of PDB 1yba Chain A

Receptor sequence
>1ybaA (length=406) Species: 562 (Escherichia coli) [Search protein sequence]
SLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDA
HFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNA
PFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKL
GIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMS
DVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALA
SKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENI
GLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLMHIHENRPGVLTAL
NKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTI
RARLLY
3D structure
PDB1yba Vmax Regulation through Domain and Subunit Changes. The Active Form of Phosphoglycerate Dehydrogenase
ChainA
Resolution2.24 Å
3D
structure
Catalytic site residues are labeled in the structure
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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.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 PO4 A G85 N87 G81 N83
BS02 AKG A R60 S61 C83 I84 R56 S57 C79 I80
BS03 NAD A I84 F106 V112 G158 G160 H161 I162 Y180 D181 I182 K185 H210 V211 P212 A238 S239 R240 H292 G294 I80 F102 V108 G154 G156 H157 I158 Y176 D177 I178 K181 H206 V207 P208 A234 S235 R236 H288 G290
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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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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