Structure of PDB 6d3i Chain A Binding Site BS02

Receptor Information
>6d3i Chain A (length=286) Species: 76947 (Sphingobium herbicidovorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NKYRFIDVQPLTGVLGAEITGVDLREPLDDSTWNEILDAFHTYQVIYFPG
QAITNEQHIAFSRRFGPVDPVPILKSIEGYPEVQMIRREANESSRYIGDD
WHADSTFLDAPPAAVVMRAIEVPEYGGDTGFLSMYSAWETLSPTMQATIE
GLNVVHSATKVFGSLYQATNWRFSNTSVKVMDVDAGDRETVHPLVVTHPV
TGRRALYCNQVYCQKIQGMTDAESKSLLQFLYEHATQFDFTCRVRWKKDQ
VLVWDNLCTMHRAVPDYAGKFRYLTRTTVAGDKPSR
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 chain6d3i Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6d3i Development of enzymes for robust aryloxyphenoxypropionate and synthetic auxin herbicide tolerance traits in maize and soybean crops.
Resolution3.196 Å
Binding residue
(original residue number in PDB)		I95 I106 D113 A272 R281 R285
Binding residue
(residue number reindexed from 1)		I86 I97 D104 A263 R272 R276
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H111 D113 H270 R285
Catalytic site (residue number reindexed from 1) H102 D104 H261 R276
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:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0009056 catabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6d3i, PDBe:6d3i, PDBj:6d3i
PDBsum6d3i
PubMed30828945
UniProtQ8KSC8|RDPA_SPHHM (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase (Gene Name=rdpA)

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