SMTL ID : 3gke.1

Crystal Structure of Dicamba Monooxygenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 10 residues within 4Å: Chain A: C.49, H.51, R.52, F.53, A.54, C.68, Y.70, H.71, G.72, L.73 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.49, A:H.51, A:C.68, A:H.71 FES.8: 10 residues within 4Å: Chain B: C.49, H.51, R.52, F.53, A.54, C.68, Y.70, H.71, G.72, L.73 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.49, B:H.51, B:C.68, B:H.71 FES.15: 10 residues within 4Å: Chain C: C.49, H.51, R.52, F.53, A.54, C.68, Y.70, H.71, G.72, L.73 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.49, C:H.51, C:C.68, C:H.71

2 x FE: FE (III) ION(Non-covalent)

FE.2: 5 residues within 4Å: Chain A: N.154, H.160, H.165, D.294 Ligands: ACT.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.160, A:H.165, A:D.294, A:D.294 FE.9: 5 residues within 4Å: Chain B: N.154, H.160, H.165, D.294 Ligands: OXY.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.160, B:H.165, B:D.294, B:D.294

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 11 residues within 4Å: Chain A: W.9, Y.10, V.11, W.110, K.224, V.225, S.226, A.227, I.252, L.253, T.254 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.11, A:K.224, A:V.225, A:S.226 EDO.4: 7 residues within 4Å: Chain A: L.14, E.16, A.107, R.130, T.137, V.138, G.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.130 Water bridges: A:G.140 EDO.5: 6 residues within 4Å: Chain A: D.126, F.127, G.128, C.129, L.229, R.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.129 Water bridges: A:G.128 EDO.12: 12 residues within 4Å: Chain B: W.9, Y.10, V.11, W.110, K.224, V.225, S.226, A.227, I.252, L.253, T.254 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.11, B:V.225, B:S.226 EDO.13: 7 residues within 4Å: Chain B: A.8, W.9, A.123, P.125, K.224, V.225 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.9, B:V.225 Water bridges: B:A.123 EDO.14: 8 residues within 4Å: Chain B: M.156, D.157, L.158, R.179, A.190, N.218, D.219, I.220 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.158, B:R.179, B:N.218, B:I.220 Water bridges: B:M.156, B:R.179, B:C.320 EDO.16: 10 residues within 4Å: Chain C: W.9, Y.10, V.11, K.224, V.225, S.226, A.227, I.252, L.253, T.254 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.11, C:K.224, C:V.225, C:S.226 EDO.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.18: 7 residues within 4Å: Chain C: L.14, E.16, A.107, R.130, T.137, V.138, G.139 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.130 Water bridges: C:G.140

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 7 residues within 4Å: Chain A: N.230, I.232, G.249, H.251, W.285, L.290 Ligands: ACT.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.232 Hydrogen bonds: A:N.230, A:N.230 Water bridges: A:G.266 Salt bridges: A:H.251 ACT.7: 10 residues within 4Å: Chain A: L.158, H.160, A.161, H.165, H.251, W.285, L.290, D.294 Ligands: FE.2, ACT.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.158 Salt bridges: A:H.160, A:H.165 ACT.11: 6 residues within 4Å: Chain B: N.230, I.232, G.249, H.251, W.285, L.290 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.232 Hydrogen bonds: B:N.230, B:W.285 Salt bridges: B:H.251 ACT.19: 3 residues within 4Å: Chain C: V.62, E.74, H.83 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.62 Salt bridges: C:H.83

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.10: 5 residues within 4Å: Chain B: H.160, H.165, L.290, D.294 Ligands: FE.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dumitru, R. et al., Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation. J.Mol.Biol. (2009)

Release Date

2009-07-21

Peptides

DdmC: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DdmC

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