SMTL ID : 5bkc.1

Crystal structure of AAD-1 in complex with (R)-diclofop, Mn(II), and 2-oxoglutarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.111, D.113, H.270 Ligands: AKG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.111, A:D.113, A:H.270 MN.6: 4 residues within 4Å: Chain B: H.111, D.113, H.270 Ligands: AKG.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.111, B:D.113, B:H.270, H2O.20

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

AKG.2: 14 residues within 4Å: Chain A: 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: MN.1, O0D.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.272 Salt bridges: A:H.270, A:R.281, A:R.285 AKG.7: 13 residues within 4Å: Chain B: 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: MN.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.138 Salt bridges: B:H.270, B:R.281, B:R.285

1 x O0D: (2R)-2-{4-[(3,5-dichloropyridin-2-yl)oxy]phenoxy}propanoic acid(Non-covalent)

O0D.3: 16 residues within 4Å: Chain A: V.80, L.82, L.83, I.106, G.107, D.108, D.109, H.111, D.113, S.114, R.169, V.170, F.182, V.220, Y.221 Ligands: AKG.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.82, A:L.83, A:I.106, A:F.182, A:V.220 Hydrogen bonds: A:G.107, A:D.108, A:D.109, A:S.114, A:Y.221 Halogen bonds: A:R.169

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: R.34, Q.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.66, A:Q.66 Water bridges: A:R.34 Salt bridges: A:R.34 SO4.5: 5 residues within 4Å: Chain A: D.109, W.110, R.271 Chain B: R.246, F.247 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.247 Salt bridges: A:R.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chekan, J.R. et al., Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-06-12

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase

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