SMTL ID : 1tmx.1

Crystal structure of hydroxyquinol 1,2-dioxygenase from Nocardioides Simplex 3E

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: Y.164, Y.197, H.221, H.223 Ligands: BEZ.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:Y.164, A:Y.197, A:H.221, A:H.223 FE.7: 5 residues within 4Å: Chain B: Y.164, Y.197, H.221, H.223 Ligands: BEZ.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:Y.164, B:Y.197, B:H.221, B:H.223

1 x CU: COPPER (II) ION(Non-covalent)

CU.2: 3 residues within 4Å: Chain A: H.42 Chain B: H.42 Ligands: CL.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.42, A:H.42

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: H.42 Chain B: H.42 Ligands: CU.2 Ligand excluded by PLIP

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

SO4.4: 4 residues within 4Å: Chain A: E.104, K.255, D.256, S.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.104, A:D.256, A:S.257 Water bridges: A:E.104 SO4.8: 3 residues within 4Å: Chain B: T.53, A.55, E.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.53, B:E.56

2 x HGX: 1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYL CHOLINE(Non-covalent)

HGX.5: 16 residues within 4Å: Chain A: L.43, F.46, L.52, E.56, W.57, T.59, G.60, F.63, L.81, M.208 Chain B: L.32, V.35, M.36, L.39, S.82 Ligands: HGX.9 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.43, A:F.46, A:L.52, A:L.52, A:E.56, A:T.59, A:F.63, A:F.63, A:L.81, B:L.32, B:V.35, B:L.39, B:L.39 HGX.9: 15 residues within 4Å: Chain A: L.32, V.35, M.36, L.39, L.81, S.82 Chain B: E.56, W.57, T.59, G.60, F.63, R.207, M.208, A.211 Ligands: HGX.5 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.59, B:F.63, B:F.63, B:F.63, A:L.32, A:V.35, A:L.39, A:L.81 Water bridges: B:T.59, A:L.32 Salt bridges: B:R.207

2 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.6: 13 residues within 4Å: Chain A: L.80, D.83, G.109, P.110, F.111, Y.164, Y.197, I.199, R.218, H.221, H.223, V.251 Ligands: FE.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.80, A:P.110, A:F.111, A:I.199, A:V.251 Water bridges: A:F.111 Salt bridges: A:R.218, A:H.221, A:H.223 BEZ.10: 14 residues within 4Å: Chain B: L.80, D.83, G.109, P.110, F.111, Y.164, Y.197, I.199, R.218, H.221, H.223, H.237, V.251 Ligands: FE.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.80, B:P.110, B:I.199, B:V.251 Water bridges: B:F.111 Salt bridges: B:R.218, B:H.221, B:H.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraroni, M. et al., Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation. J.Biol.Chem. (2005)

Release Date

2005-03-22

Peptides

hydroxyquinol 1,2-dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

hydroxyquinol 1,2-dioxygenase