Structure of PDB 5k87 Chain A Binding Site BS01

Receptor Information
>5k87 Chain A (length=389) Species: 211586 (Shewanella oneidensis MR-1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSP
DPYAKQIDGMGGATSSTSETVILSHSSKANHDVDYLFGQVSIDKPFVDWS
GNCGNLTAAVGAFAISNGLIDAARIPRNGVCTVRIWQANIGKTIIAHVPI
TDGAVQETGDFELDGVTFPAAEVQIEFMNPAADGGCMFPTGNLVDVLEVP
GIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDNAALAKFETIRA
HGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLLV
RALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSG
TLRVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPKP
Ligand information
Ligand IDMLI
InChIInChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)/p-2
InChIKeyOFOBLEOULBTSOW-UHFFFAOYSA-L
SMILES
SoftwareSMILES
ACDLabs 10.04
CACTVS 3.341		[O-]C(=O)CC([O-])=O
OpenEye OEToolkits 1.5.0C(C(=O)[O-])C(=O)[O-]
FormulaC3 H2 O4
NameMALONATE ION
ChEMBL
DrugBankDB02201
ZINC
PDB chain5k87 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5k87 The PrpF protein of Shewanella oneidensis MR-1 catalyzes the isomerization of 2-methyl-cis-aconitate during the catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle.
Resolution1.219 Å
Binding residue
(original residue number in PDB)		T68 S69 S70 H317 H318
Binding residue
(residue number reindexed from 1)		T64 S65 S66 H309 H310
Annotation score2
Enzymatic activity
Enzyme Commision number 5.3.3.-
Gene Ontology
Molecular Function
GO:0016853 isomerase activity
GO:0016863 intramolecular oxidoreductase activity, transposing C=C bonds
Biological Process
GO:0019629 propionate catabolic process, 2-methylcitrate cycle

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Molecular Function
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Biological Process
External links
PDB RCSB:5k87, PDBe:5k87, PDBj:5k87
PDBsum5k87
PubMed29145506
UniProtQ8EJW4|PRPF_SHEON 2-methyl-aconitate isomerase (Gene Name=prpF)

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