SMTL ID : 6d0o.1

rdpA dioxygenase holoenzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x CO: COBALT (II) ION(Non-covalent)

CO.1: 4 residues within 4Å: Chain A: H.111, D.113, H.270 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.111, A:D.113, A:H.270, H2O.4 CO.3: 4 residues within 4Å: Chain B: H.111, D.113, H.270 Ligands: AKG.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.111, B:D.113, B:H.270 CO.5: 4 residues within 4Å: Chain C: H.111, D.113, H.270 Ligands: AKG.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.111, C:D.113, C:H.270, H2O.14 CO.7: 4 residues within 4Å: Chain D: H.111, D.113, H.270 Ligands: AKG.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.111, D:D.113, D:H.270, H2O.19

4 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 11 residues within 4Å: Chain A: G.107, H.111, D.113, M.126, T.138, W.255, W.263, H.270, R.281, R.285 Ligands: CO.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.107, A:T.138, A:T.138 Water bridges: A:I.273 Salt bridges: A:H.270, A:R.281, A:R.285 AKG.4: 10 residues within 4Å: Chain B: G.107, H.111, D.113, M.126, T.138, H.270, A.272, R.281, R.285 Ligands: CO.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.285 Water bridges: B:I.273, B:R.281, B:R.281 Salt bridges: B:H.111, B:H.270, B:R.281 AKG.6: 13 residues within 4Å: Chain C: I.95, I.106, G.107, H.111, D.113, M.126, T.138, W.263, H.270, A.272, R.281, R.285 Ligands: CO.5 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.272 Water bridges: C:I.273 Salt bridges: C:H.270, C:R.281, C:R.285 AKG.8: 12 residues within 4Å: Chain D: I.95, I.106, G.107, H.111, D.113, M.126, T.138, H.270, A.272, R.281, R.285 Ligands: CO.7 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.272 Hydrogen bonds: D:T.138 Water bridges: D:I.273 Salt bridges: D:H.270, D:R.281, D:R.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larue, C.T. et al., Development of enzymes for robust aryloxyphenoxypropionate and synthetic auxin herbicide tolerance traits in maize and soybean crops. Pest Manag. Sci. (2019)

Release Date

2018-08-15

Peptides

(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase