SMTL ID : 3fah.2 (1 other biounit)

Glycerol inhibited form of Aldehyde oxidoreductase from Desulfovibrio gigas

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 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.37, H2O.470, H2O.549 MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 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.1145, H2O.1578, H2O.1657 MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.2: 3 residues within 4Å: Chain A: Y.897, P.898, E.899 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: Y.892, R.893 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: R.460, L.498, F.532, Y.535, G.536, Q.539 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: Y.897, P.898, E.899 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: Y.892, R.893 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain B: R.460, L.498, F.532, Y.535, G.536, Q.539 Ligand excluded by PLIP

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

FES.7: 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.8: 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.19: 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.20: 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 PCD: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)(Non-covalent)

PCD.9: 38 residues within 4Å: Chain A: Q.99, C.139, I.390, G.419, T.420, F.421, G.422, A.531, F.532, R.533, W.650, H.653, G.654, Q.655, G.656, A.657, 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: GOL.12 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Q.701 Hydrogen bonds: A:Q.99, A:T.420, A:F.421, A:F.421, A:H.653, 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.21: 38 residues within 4Å: Chain B: Q.99, C.139, I.390, G.419, T.420, F.421, G.422, A.531, F.532, R.533, W.650, H.653, G.654, Q.655, G.656, A.657, 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: GOL.24 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Q.701 Hydrogen bonds: B:Q.99, B:T.420, B:F.421, B:F.421, B:H.653, 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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: L.193, P.416, W.683 Chain B: V.5, E.12, N.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.12 Water bridges: B:Q.3, B:Q.3, B:E.12, B:N.14, B:N.14 GOL.11: 5 residues within 4Å: Chain A: K.884, G.888, V.889, R.890, Y.892 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.884, A:K.884, A:R.890 GOL.12: 8 residues within 4Å: Chain A: F.425, A.531, Y.535, Y.622, G.696, G.697, E.869 Ligands: PCD.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.622, A:Y.622, A:G.697 GOL.22: 6 residues within 4Å: Chain A: V.5, E.12, N.14 Chain B: L.193, P.416, W.683 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.3, A:Q.3, A:E.12, A:N.14, A:N.14 GOL.23: 5 residues within 4Å: Chain B: K.884, G.888, V.889, R.890, Y.892 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.884, B:K.884, B:R.890, B:Y.892 GOL.24: 8 residues within 4Å: Chain B: F.425, A.531, Y.535, Y.622, G.696, G.697, E.869 Ligands: PCD.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.622, B:G.697

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santos-Silva, T. et al., Kinetic, structural, and EPR studies reveal that aldehyde oxidoreductase from Desulfovibrio gigas does not need a sulfido ligand for catalysis and give evidence for a direct Mo-C interaction in a biological system. J.Am.Chem.Soc. (2009)

Release Date

2009-10-06

Peptides

Aldehyde oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Aldehyde oxidoreductase

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