Structure of PDB 4b5w Chain D Binding Site BS02

Receptor Information
>4b5w Chain D (length=253) Species: 481805 (Escherichia coli ATCC 8739) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNV
QTVLTQLQAIAPYPSQPVVAPSWNDPVQIKQLLDVGTQTLLVPMVQNADE
AREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIET
REAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIV
QIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARF
GAQ
Ligand information
Ligand IDPYR
InChIInChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)
InChIKeyLCTONWCANYUPML-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)C(O)=O
OpenEye OEToolkits 1.7.6CC(=O)C(=O)O
ACDLabs 12.01O=C(C(=O)O)C
FormulaC3 H4 O3
NamePYRUVIC ACID
ChEMBLCHEMBL1162144
DrugBankDB00119
ZINCZINC000001532517
PDB chain4b5w Chain D Residue 1256 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4b5w Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity
Resolution1.792 Å
Binding residue
(original residue number in PDB)		Q147 E149 G172 P173 A174 D175
Binding residue
(residue number reindexed from 1)		Q147 E149 G172 P173 A174 D175
Annotation score5
Binding affinityMOAD: Kd=26.9mM
Enzymatic activity
Catalytic site (original residue number in PDB) H45 A70 D84 E149 D175
Catalytic site (residue number reindexed from 1) H45 A70 D84 E149 D175
Enzyme Commision number 4.1.2.52: 4-hydroxy-2-oxoheptanedioate aldolase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016829 lyase activity
GO:0016832 aldehyde-lyase activity
GO:0043863 4-hydroxy-2-ketopimelate aldolase activity
GO:0046872 metal ion binding
GO:0061677 2-dehydro-3-deoxy-D-gluconate aldolase activity
Biological Process
GO:0009056 catabolic process
GO:0010124 phenylacetate catabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4b5w, PDBe:4b5w, PDBj:4b5w
PDBsum4b5w
PubMed22908224
UniProtB1IS70|HPCH_ECOLC 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase (Gene Name=hpcH)

[Back to BioLiP]