Structure of PDB 1ebg Chain B Binding Site BS02

Receptor Information
>1ebg Chain B (length=436) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGASTGVHEALEMRD
GDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVKDQKAVDDFLISLDGTA
NKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPF
LNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKR
YGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKVKIGLDCASS
EFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAE
DDWEAWSHFFKTAGIQIVADDLTVTNPKRIATAIEKKAADALLLKVNQIG
TLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAP
ARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKL
Ligand information
Ligand IDPAH
InChIInChI=1S/C2H6NO5P/c4-2(3-5)1-9(6,7)8/h5H,1H2,(H,3,4)(H2,6,7,8)
InChIKeyLDKRAXXVBWHMRH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NO)CP(=O)(O)O
CACTVS 3.341ONC(=O)C[P](O)(O)=O
OpenEye OEToolkits 1.5.0C(C(=O)NO)P(=O)(O)O
FormulaC2 H6 N O5 P
NamePHOSPHONOACETOHYDROXAMIC ACID
ChEMBLCHEMBL328944
DrugBankDB03645
ZINCZINC000005828202
PDB chain1ebg Chain B Residue 440 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ebg Chelation of serine 39 to Mg2+ latches a gate at the active site of enolase: structure of the bis(Mg2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1-A resolution.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		A38 S39 H159 Q167 E168 D246 D320 K345 R374 S375 K396
Binding residue
(residue number reindexed from 1)		A38 S39 H159 Q167 E168 D246 D320 K345 R374 S375 K396
Annotation score1
Binding affinityMOAD: Ki=15pM
Enzymatic activity
Catalytic site (original residue number in PDB) S39 H159 E168 E211 D246 E295 D320 K345 H373 K396
Catalytic site (residue number reindexed from 1) S39 H159 E168 E211 D246 E295 D320 K345 H373 K396
Enzyme Commision number 4.2.1.11: phosphopyruvate hydratase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004634 phosphopyruvate hydratase activity
GO:0016829 lyase activity
GO:0046872 metal ion binding
GO:1904408 melatonin binding
Biological Process
GO:0006096 glycolytic process
GO:0032889 regulation of vacuole fusion, non-autophagic
Cellular Component
GO:0000015 phosphopyruvate hydratase complex
GO:0000324 fungal-type vacuole
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ebg, PDBe:1ebg, PDBj:1ebg
PDBsum1ebg
PubMed8049235
UniProtP00924|ENO1_YEAST Enolase 1 (Gene Name=ENO1)

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