Structure of PDB 5bkd Chain B Binding Site BS02

Receptor Information
>5bkd Chain B (length=267) Species: 80866 (Delftia acidovorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RFERIAVQPLTGVLGAEITGVDLREPLDDSTWNEILDAFHTYQVIYFPGQ
AITNEQHIAFSRRFGPVDPVPLLKSIEGYPEVQMIRREANESGRVIGDDW
HTDSTFLDAPPAAVVMRAIDVPEHGGDTGFLSMYTAWETLSPTMQATIEG
LNVVHSATRVFGSLDAGDRETVHPLVVTHPGSGRKGLYVNQVYCQRIEGM
TDAESKPLLQFLYEHATRFDFTCRVRWKKDQVLVWDNLCTMHRAVPDYAG
KFRYLTRTTVGGVRPAR
Ligand information
Ligand IDAKG
InChIInChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
InChIKeyKPGXRSRHYNQIFN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(=O)CCC(=O)O
OpenEye OEToolkits 1.7.6C(CC(=O)O)C(=O)C(=O)O
CACTVS 3.385OC(=O)CCC(=O)C(O)=O
FormulaC5 H6 O5
Name2-OXOGLUTARIC ACID
ChEMBLCHEMBL1686
DrugBankDB08845
ZINCZINC000001532519
PDB chain5bkd Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5bkd Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		I95 H111 D113 T138 H270 A272 R281 R285
Binding residue
(residue number reindexed from 1)		I85 H101 D103 T128 H242 A244 R253 R257
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H111 D113 H270 R285
Catalytic site (residue number reindexed from 1) H101 D103 H242 R257
Enzyme Commision number 1.14.11.44: (R)-dichlorprop dioxygenase (2-oxoglutarate).
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016706 2-oxoglutarate-dependent dioxygenase activity
GO:0031418 L-ascorbic acid binding
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:5bkd, PDBe:5bkd, PDBj:5bkd
PDBsum5bkd
PubMed31209034
UniProtP83310|RDPA_DELAC (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase (Gene Name=rdpA)

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