Structure of PDB 2zyd Chain B Binding Site BS01

Receptor Information
>2zyd Chain B (length=466) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKL
VPYYTVKEFVESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGG
NTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSIMPGGQKEAYEL
VAPILTKIAAVAEDGEPCVTYIGADGAGHYVKMVHNGIEYGDMQLIAEAY
SLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFTKKDEDGNYLVD
VILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAASK
VLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDL
NYGEIAKIFRAGCIIRAQFLQKITDACAENPQIANLLLAPYFKQIADDYQ
QALRDVVAYAVQNGIPVPTFSAAVAYYDSYRAAVLPANLIQAQRDYFGAH
TYKRIDKEGVFHTEWL
Ligand information
Ligand IDGLO
InChIInChI=1S/C6H12O6/c7-1-3(9)5(11)6(12)4(10)2-8/h1,3-6,8-12H,2H2/t3-,4+,5+,6+/m0/s1
InChIKeyGZCGUPFRVQAUEE-SLPGGIOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH](O)[CH](O)[CH](O)[CH](O)C=O
OpenEye OEToolkits 1.5.0C([C@H]([C@H]([C@@H]([C@H](C=O)O)O)O)O)O
ACDLabs 10.04O=CC(O)C(O)C(O)C(O)CO
OpenEye OEToolkits 1.5.0C(C(C(C(C(C=O)O)O)O)O)O
CACTVS 3.341OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C=O
FormulaC6 H12 O6
NameD-glucose;
D-GLUCOSE IN LINEAR FORM
ChEMBLCHEMBL448805
DrugBankDB01914
ZINCZINC000100009383
PDB chain2zyd Chain A Residue 3929 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2zyd Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism
Resolution1.5 Å
Binding residue
(original residue number in PDB)
E190 K260 R287
Binding residue
(residue number reindexed from 1)
E189 K259 R286
Annotation score1
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).
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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:2zyd, PDBe:2zyd, PDBj:2zyd
PDBsum2zyd
PubMed19686854
UniProtP00350|6PGD_ECOLI 6-phosphogluconate dehydrogenase, decarboxylating (Gene Name=gnd)

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