Structure of PDB 6d3m Chain A

Receptor sequence

>6d3mA (length=286) Species: 76947 (Sphingobium herbicidovorans)

NKYRFIDVQPLTGVLGAEITGVDLREPLDDSTWNEILDAFHTYQVIYFPG
QAITNEQHIAFSRRFGPVDPVPILKSIEGYPEVQMIRREANESSRFIGDD
WHTDSTFLDAPPAAVVMRAIEVPEYGGDTGFLSMYSAWETLSPTMQATIE
GLNVVHSATKVFGSLYQATNWRFSNTSVKVMDVDAGDRETVHPLVVTHPV
TGRRALYCNQVYCQKIQGMTDAESKSLLQFLYEHATKFDFTCRVRWKKDQ
VLVWDNLCTMHRAVPDYAGKFRYLTRTTVAGDKPSR

3D structure

• PDB: 6d3m Development of enzymes for robust aryloxyphenoxypropionate and synthetic auxin herbicide tolerance traits in maize and soybean crops.
• Chain: A
• Resolution: 2.03 Å

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).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	CO	A	H111 D113 H270	H102 D104 H261
BS02	FTJ	A	I82 R104 G107 H111 D113 S114 K169 W180 V220 Y221	I73 R95 G98 H102 D104 S105 K160 W171 V211 Y212
BS03	AKG	A	I95 H111 D113 T138 H270 A272 R281 R285	I86 H102 D104 T129 H261 A263 R272 R276

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:6d3m, PDBe:6d3m, PDBj:6d3m
• PDBsum: 6d3m
• PubMed: 30828945
• UniProt: Q8KSC8|RDPA_SPHHM (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase (Gene Name=rdpA)