SMTL ID : 4us8.1

Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with benzaldehyde

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 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.17: 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.18: 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 PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 7 residues within 4Å: Chain A: L.254, H.393, L.394, Y.397, N.691 Ligands: HBX.14, HBX.16 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.394, A:N.691 PGE.19: 7 residues within 4Å: Chain B: L.254, H.393, L.394, Y.397, N.691 Ligands: HBX.30, HBX.32 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.394, B:N.691

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

IPA.4: 5 residues within 4Å: Chain A: K.884, G.888, V.889, R.890, Y.892 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.890, A:Y.892 Hydrogen bonds: A:G.888, A:R.890 IPA.20: 5 residues within 4Å: Chain B: K.884, G.888, V.889, R.890, Y.892 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.890, B:Y.892 Hydrogen bonds: B:G.888, B:R.890

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

BCT.5: 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.21: 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

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

MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: D.263 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.263, H2O.25, H2O.25, H2O.49 MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 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) MG.24: 1 residues within 4Å: Chain B: D.263 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.263, H2O.74, H2O.74, H2O.98 MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 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.26: 2 residues within 4Å: Chain B: Y.892, R.893 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: Y.897, P.898, E.899 Ligand excluded by PLIP

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

PCD.12: 37 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: HBX.13, HBX.15 23 PLIP interactions: 23 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:G.697, 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.28: 37 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: HBX.29, HBX.31 22 PLIP interactions: 22 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:G.697, 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, B:E.869 Water bridges: B:R.533

8 x HBX: benzaldehyde(Non-covalent)

HBX.13: 11 residues within 4Å: Chain A: F.425, L.497, R.501, A.531, Y.535, L.626, D.627, G.697 Ligands: PCD.12, HBX.15, HBX.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.497, A:A.531, A:L.626 Hydrogen bonds: A:R.501, A:D.627 pi-Stacking: A:F.425, A:Y.535 HBX.14: 8 residues within 4Å: Chain A: I.255, L.394, F.425, F.494, L.626, P.694 Ligands: PGE.3, HBX.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.255, A:L.394, A:F.425, A:F.494, A:L.626 Water bridges: A:N.691 HBX.15: 12 residues within 4Å: Chain A: F.425, L.497, R.501, A.531, Y.535, L.626, G.696, G.697, E.869 Ligands: PCD.12, HBX.13, HBX.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.497, A:A.531, A:L.626 Hydrogen bonds: A:G.697 pi-Stacking: A:F.425, A:Y.535 HBX.16: 9 residues within 4Å: Chain A: I.255, L.394, F.425, L.497, L.626 Ligands: PGE.3, HBX.13, HBX.14, HBX.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.255, A:L.394, A:F.425, A:L.626 Water bridges: A:D.627 HBX.29: 11 residues within 4Å: Chain B: F.425, L.497, R.501, A.531, Y.535, L.626, D.627, G.697 Ligands: PCD.28, HBX.31, HBX.32 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.497, B:A.531, B:L.626 Hydrogen bonds: B:R.501, B:D.627, B:D.627 pi-Stacking: B:F.425, B:Y.535 HBX.30: 8 residues within 4Å: Chain B: I.255, L.394, F.425, F.494, L.626, P.694 Ligands: PGE.19, HBX.32 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.255, B:L.394, B:F.425, B:F.494, B:L.626 Water bridges: B:N.691 HBX.31: 12 residues within 4Å: Chain B: F.425, L.497, R.501, A.531, Y.535, L.626, G.696, G.697, E.869 Ligands: PCD.28, HBX.29, HBX.32 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.497, B:A.531, B:L.626 Hydrogen bonds: B:G.697 pi-Stacking: B:F.425, B:Y.535 HBX.32: 9 residues within 4Å: Chain B: I.255, L.394, F.425, L.497, L.626 Ligands: PGE.19, HBX.29, HBX.30, HBX.31 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.255, B:L.394, B:F.425, B:L.626 Water bridges: B:D.627

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Correia, H.D. et al., Aromatic Aldehydes at the Active Site of Aldehyde Oxidoreductase from Desulfovibrio Gigas: Reactivity and Molecular Details of the Enzyme-Substrate and Enzyme-Product Interaction. J.Biol.Inorg.Chem. (2015)

Release Date

2014-10-08

Peptides

ALDEHYDE OXIDOREDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ALDEHYDE OXIDOREDUCTASE

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