SMTL ID : 4c80.1

Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with hydrogen peroxide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

FES.1: 9 residues within 4Å: Chain A: G.97, Q.99, C.100, G.101, C.103, C.137, R.138, C.139, I.368 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.100, A:C.103, A:C.137, A:C.139 FES.2: 11 residues within 4Å: Chain A: V.38, G.39, C.40, E.41, G.43, Q.44, C.45, G.46, C.48, R.58, C.60 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.40, A:C.45, A:C.48, A:C.60 FES.15: 9 residues within 4Å: Chain B: G.97, Q.99, C.100, G.101, C.103, C.137, R.138, C.139, I.368 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.100, B:C.103, B:C.137, B:C.139 FES.16: 11 residues within 4Å: Chain B: V.38, G.39, C.40, E.41, G.43, Q.44, C.45, G.46, C.48, R.58, C.60 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.40, B:C.45, B:C.48, B:C.60

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 5 residues within 4Å: Chain A: K.884, G.888, V.889, R.890, Y.892 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.890, A:Y.892 Hydrogen bonds: A:K.884, A:R.890 Water bridges: A:E.553, A:Y.892 IPA.17: 5 residues within 4Å: Chain B: K.884, G.888, V.889, R.890, Y.892 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.890, B:Y.892 Hydrogen bonds: B:K.884, B:R.890 Water bridges: B:E.553, B:K.884

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.4: 9 residues within 4Å: Chain A: R.460, S.461, L.498, S.530, A.531, F.532, Y.535, G.536, Q.539 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.461, A:F.532, A:F.532 Water bridges: A:S.461 BCT.18: 9 residues within 4Å: Chain B: R.460, S.461, L.498, S.530, A.531, F.532, Y.535, G.536, Q.539 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.461, B:F.532, B:F.532 Water bridges: B:S.461

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: Q.29 Ligands: NA.19 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.29, A:Q.29, A:L.201 NA.6: 4 residues within 4Å: Chain A: Q.214, K.216, Q.452, Q.455 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.455 Water bridges: A:K.216, A:K.216, A:N.449 NA.19: 2 residues within 4Å: Chain B: Q.29 Ligands: NA.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.29 NA.20: 4 residues within 4Å: Chain B: Q.214, K.216, Q.452, Q.455 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.214 Water bridges: B:K.216, B:K.216, B:N.449

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.7: 2 residues within 4Å: Chain A: E.899, E.903 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.899, A:E.903, H2O.42, H2O.42, H2O.42 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain B: E.899, E.903 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.899, B:E.903, H2O.84, H2O.84, H2O.85 MG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.10: 2 residues within 4Å: Chain A: Y.892, R.893 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: Y.897, P.898, E.899 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: D.342, T.343, G.344 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: Y.892, R.893 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain B: Y.897, P.898, E.899 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: D.342, T.343, G.344 Ligand excluded by PLIP

2 x PCD: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)(Non-covalent)

PCD.13: 36 residues within 4Å: Chain A: Q.99, C.139, G.419, T.420, F.421, G.422, A.531, F.532, R.533, W.650, H.653, G.654, Q.655, G.656, G.660, S.695, G.696, G.697, S.698, R.699, Q.700, Q.701, L.795, S.797, L.798, C.799, N.800, T.804, Q.807, A.864, S.865, G.866, V.867, G.868, E.869 Ligands: PEO.14 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Q.701, A:V.867 Hydrogen bonds: A:Q.99, A:T.420, A:F.421, A:F.421, A:H.653, A:H.653, A:Q.655, A:G.656, A:R.699, A:Q.700, A:Q.701, A:Q.701, A:S.797, A:C.799, A:N.800, A:Q.807, A:V.867, A:G.868, A:E.869 Water bridges: A:R.533 PCD.27: 36 residues within 4Å: Chain B: Q.99, C.139, G.419, T.420, F.421, G.422, A.531, F.532, R.533, W.650, H.653, G.654, Q.655, G.656, G.660, S.695, G.696, G.697, S.698, R.699, Q.700, Q.701, L.795, S.797, L.798, C.799, N.800, T.804, Q.807, A.864, S.865, G.866, V.867, G.868, E.869 Ligands: PEO.28 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Q.701, B:V.867 Hydrogen bonds: B:Q.99, B:T.420, B:F.421, B:F.421, B:H.653, B:Q.655, B:G.656, B:R.699, B:Q.700, B:Q.701, B:Q.701, B:S.797, B:C.799, B:N.800, B:Q.807, B:V.867, B:G.868 Water bridges: B:R.533

2 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.14: 5 residues within 4Å: Chain A: A.531, G.696, G.697, E.869 Ligands: PCD.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.697 PEO.28: 5 residues within 4Å: Chain B: A.531, G.696, G.697, E.869 Ligands: PCD.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.697

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marangon, J. et al., Kinetic and Structural Studies of Aldehyde Oxidoreductase from Desulfovibrio Gigas Reveal a Dithiolene-Based Chemistry for Enzyme Activation and Inhibition by H2O2. Plos One (2013)

Release Date

2014-01-15

Peptides

ALDEHYDE OXIDOREDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ALDEHYDE OXIDOREDUCTASE

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