Structure of PDB 4onv Chain D Binding Site BS01

Receptor Information
>4onv Chain D (length=298) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFS
QLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADG
IVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVK
TLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTL
LLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQL
DTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC
Ligand information
Ligand IDKDG
InChIInChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5+/m0/s1
InChIKeyWPAMZTWLKIDIOP-WVZVXSGGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O
CACTVS 3.341OC[C@@H](O)[C@@H](O)CC(=O)C(O)=O
ACDLabs 10.04O=C(C(=O)O)CC(O)C(O)CO
CACTVS 3.341OC[CH](O)[CH](O)CC(=O)C(O)=O
OpenEye OEToolkits 1.5.0C(C(C(CO)O)O)C(=O)C(=O)O
FormulaC6 H10 O6
Name2-KETO-3-DEOXYGLUCONATE
ChEMBL
DrugBank
ZINCZINC000001532568
PDB chain4onv Chain D Residue 409 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4onv Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.
Resolution2.57 Å
Binding residue
(original residue number in PDB)		P20 G55 S56 G57 Y145 K174 T176 G202 A221
Binding residue
(residue number reindexed from 1)		P9 G44 S45 G46 Y134 K163 T165 G191 A210
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) S56 Y119 Y145 L150 K174 I219
Catalytic site (residue number reindexed from 1) S45 Y108 Y134 L139 K163 I208
Enzyme Commision number 4.1.2.28: 2-dehydro-3-deoxy-D-pentonate aldolase.
4.1.2.51: 2-dehydro-3-deoxy-D-gluconate aldolase.
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0042802 identical protein binding
GO:0047440 2-dehydro-3-deoxy-D-pentonate aldolase activity
GO:0061677 2-dehydro-3-deoxy-D-gluconate aldolase activity
Biological Process
GO:0046176 aldonic acid catabolic process
Cellular Component
GO:0005737 cytoplasm
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:4onv, PDBe:4onv, PDBj:4onv
PDBsum4onv
PubMed
UniProtP75682|YAGE_ECOLI Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE (Gene Name=yagE)

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