Structure of PDB 4ptn Chain D Binding Site BS01

Receptor Information
>4ptn 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 IDGXV
InChIInChI=1S/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2/t3-/m1/s1
InChIKeyMNQZXJOMYWMBOU-GSVOUGTGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C([C@@H](C=O)O)O
CACTVS 3.385OC[C@H](O)C=O
ACDLabs 12.01OCC(O)C=O
OpenEye OEToolkits 2.0.7C(C(C=O)O)O
CACTVS 3.385OC[CH](O)C=O
FormulaC3 H6 O3
NameL-glyceraldehyde;
Glyceraldehyde;
(2S)-2,3-dihydroxypropanal
ChEMBL
DrugBank
ZINCZINC000000901286
PDB chain4ptn Chain D Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ptn Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		K174 G202 Y203 S220 A221 F265
Binding residue
(residue number reindexed from 1)		K163 G191 Y192 S209 A210 F254
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:4ptn, PDBe:4ptn, PDBj:4ptn
PDBsum4ptn
PubMed18361457
UniProtP75682|YAGE_ECOLI Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE (Gene Name=yagE)

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