Structure of PDB 6d3j Chain A Binding Site BS04

Receptor Information

>6d3j Chain A (length=247) Species: 76947 (Sphingobium herbicidovorans)

NKYRFIDVQPLTGVLGAEITGVDLREPLDDSTWNEILDAFHTYQVIYFPG
QAITNEQHIAFSRRFGPVDPVPILKSIEGYPEVQMIRIGDDWHTDSTFLD
APPAAVVMRAIEVPEYGGDTGFLSMYSAWETLSPTMQATIEGLNVVHSAE
TVHPLVVTHPVTGRRALYCNQVYCQKIQGMTDAESKSLLQFLYEHATKFD
FTCRVRWKKDQVLVWDNLCTMHRAVPDYAGKFRYLTRTTVAGDKPSR

Ligand information

• Ligand ID: CO
• InChI: InChI=1S/Co/q+2
• InChIKey: XLJKHNWPARRRJB-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Co+2]
  CACTVS 3.341: [Co++]
• Formula: Co
• Name: COBALT (II) ION
• DrugBank: DB14205
• PDB chain: 6d3j Chain A Residue 311

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6d3j Development of enzymes for robust aryloxyphenoxypropionate and synthetic auxin herbicide tolerance traits in maize and soybean crops.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): D108 D109
• Binding residue (residue number reindexed from 1): D90 D91
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H111 D113 H270 R285
• Catalytic site (residue number reindexed from 1): H93 D95 H222 R237
• 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

External links

• PDB: RCSB:6d3j, PDBe:6d3j, PDBj:6d3j
• PDBsum: 6d3j
• PubMed: 30828945
• UniProt: Q8KSC8|RDPA_SPHHM (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase (Gene Name=rdpA)