Structure of PDB 6d3m Chain A Binding Site BS01

Receptor Information
>6d3m 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
QAITNEQHIAFSRRFGPVDPVPILKSIEGYPEVQMIRREANESSRFIGDD
WHTDSTFLDAPPAAVVMRAIEVPEYGGDTGFLSMYSAWETLSPTMQATIE
GLNVVHSATKVFGSLYQATNWRFSNTSVKVMDVDAGDRETVHPLVVTHPV
TGRRALYCNQVYCQKIQGMTDAESKSLLQFLYEHATKFDFTCRVRWKKDQ
VLVWDNLCTMHRAVPDYAGKFRYLTRTTVAGDKPSR
Ligand information
Ligand IDCO
InChIInChI=1S/Co/q+2
InChIKeyXLJKHNWPARRRJB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Co+2]
CACTVS 3.341[Co++]
FormulaCo
NameCOBALT (II) ION
ChEMBL
DrugBankDB14205
ZINC
PDB chain6d3m Chain A Residue 301 [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]
PDB6d3m Development of enzymes for robust aryloxyphenoxypropionate and synthetic auxin herbicide tolerance traits in maize and soybean crops.
Resolution2.03 Å
Binding residue
(original residue number in PDB)		H111 D113 H270
Binding residue
(residue number reindexed from 1)		H102 D104 H261
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6d3m, PDBe:6d3m, PDBj:6d3m
PDBsum6d3m
PubMed30828945
UniProtQ8KSC8|RDPA_SPHHM (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase (Gene Name=rdpA)

[Back to BioLiP]