Structure of PDB 2zyd Chain B

Receptor sequence
>2zydB (length=466) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
SKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKL
VPYYTVKEFVESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGG
NTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSIMPGGQKEAYEL
VAPILTKIAAVAEDGEPCVTYIGADGAGHYVKMVHNGIEYGDMQLIAEAY
SLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFTKKDEDGNYLVD
VILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAASK
VLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDL
NYGEIAKIFRAGCIIRAQFLQKITDACAENPQIANLLLAPYFKQIADDYQ
QALRDVVAYAVQNGIPVPTFSAAVAYYDSYRAAVLPANLIQAQRDYFGAH
TYKRIDKEGVFHTEWL
3D structure
PDB2zyd Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism
ChainB
Resolution1.5 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) S128 K183 H186 N187 E190
Catalytic site (residue number reindexed from 1) S127 K182 H185 N186 E189
Enzyme Commision number 1.1.1.44: phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating).
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 GLO B E190 K260 R287 E189 K259 R286
Gene Ontology
Molecular Function
GO:0004616 phosphogluconate dehydrogenase (decarboxylating) 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:0042803 protein homodimerization activity
GO:0050661 NADP binding
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0006098 pentose-phosphate shunt
GO:0009051 pentose-phosphate shunt, oxidative branch
GO:0016054 organic acid catabolic process
GO:0019521 D-gluconate metabolic process
GO:0046177 D-gluconate catabolic 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:2zyd, PDBe:2zyd, PDBj:2zyd
PDBsum2zyd
PubMed19686854
UniProtP00350|6PGD_ECOLI 6-phosphogluconate dehydrogenase, decarboxylating (Gene Name=gnd)

[Back to BioLiP]