SMTL ID : 3l4p.2 (1 other biounit)

Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MOP) of Desulfovibrio gigas covalently bound to [AsO3]-

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

FES.1: 8 residues within 4Å: Chain A: 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.25: 8 residues within 4Å: Chain B: 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.26: 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

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

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 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.29, H2O.29, H2O.55 MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.30: 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.85, H2O.85, H2O.110 MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x LI: LITHIUM ION(Non-covalent)

LI.8: 5 residues within 4Å: Chain A: A.649, E.651, G.693, P.694, Q.700 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.649, A:E.651, A:E.651, A:G.693, H2O.12 LI.32: 5 residues within 4Å: Chain B: A.649, E.651, G.693, P.694, Q.700 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.649, B:E.651, B:E.651, B:G.693, H2O.67

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

CL.9: 4 residues within 4Å: Chain A: F.257, P.258, T.259, A.755 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: F.167, P.170, S.178, K.179 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: R.123, M.150 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: Y.892, R.893 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: Y.897, P.898, E.899 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: K.472, K.473, D.474 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: M.1, D.18, A.19 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: D.342, T.343, G.344 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: D.826, I.827, K.828, K.829 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain B: F.257, P.258, T.259, A.755 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain B: F.167, P.170, S.178, K.179 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain B: R.123, M.150 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain B: Y.892, R.893 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain B: Y.897, P.898, E.899 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain B: K.472, K.473, D.474 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain B: M.1, D.18, A.19 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain B: D.342, T.343, G.344 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain B: D.826, I.827, K.828, K.829 Ligand excluded by PLIP

2 x URE: UREA(Non-functional Binders)

URE.17: 9 residues within 4Å: Chain A: R.460, S.461, L.498, S.530, A.531, F.532, Y.535, G.536, Q.539 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.460, A:S.461, A:F.532, A:F.532, A:Y.535, A:G.536, A:Q.539 Water bridges: A:S.461 URE.41: 9 residues within 4Å: Chain B: R.460, S.461, L.498, S.530, A.531, F.532, Y.535, G.536, Q.539 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.460, B:S.461, B:F.532, B:F.532, B:Y.535, B:G.536, B:Q.539 Water bridges: B:S.461

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

PCD.19: 38 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, 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: AST.20, IPA.21 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Q.701, A:V.867 Hydrogen bonds: A:T.420, A:F.421, A:H.653, A:G.654, 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:Q.807, A:V.867, A:G.868, A:E.869, A:E.869 Water bridges: A:R.533 PCD.43: 38 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, 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: AST.44, IPA.45 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Q.701, B:V.867 Hydrogen bonds: B:T.420, B:F.421, B:H.653, B:G.654, 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:Q.807, B:V.867, B:G.868, B:E.869 Water bridges: B:R.533

2 x AST: ARSENITE(Non-covalent)

AST.20: 9 residues within 4Å: Chain A: F.425, A.531, Y.535, Y.622, G.696, G.697, E.869 Ligands: PCD.19, IPA.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.622, A:G.697, A:E.869 AST.44: 9 residues within 4Å: Chain B: F.425, A.531, Y.535, Y.622, G.696, G.697, E.869 Ligands: PCD.43, IPA.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.697, B:E.869

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

IPA.21: 8 residues within 4Å: Chain A: F.425, R.501, A.531, Y.535, L.626, G.697 Ligands: PCD.19, AST.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.425, A:F.425, A:A.531, A:L.626 Hydrogen bonds: A:G.697 Water bridges: A:R.501 IPA.22: 4 residues within 4Å: Chain A: L.254, L.394, Y.397, N.691 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.254, A:Y.397 Hydrogen bonds: A:N.691, A:N.691 Water bridges: A:L.394 IPA.23: 3 residues within 4Å: Chain A: I.255, L.626, P.694 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.255, A:L.626 IPA.45: 8 residues within 4Å: Chain B: F.425, R.501, A.531, Y.535, L.626, G.697 Ligands: PCD.43, AST.44 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.425, B:F.425, B:A.531, B:L.626 Hydrogen bonds: B:G.697 Water bridges: B:R.501 IPA.46: 4 residues within 4Å: Chain B: L.254, L.394, Y.397, N.691 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.254, B:Y.397 Hydrogen bonds: B:N.691, B:N.691 Water bridges: B:L.394 IPA.47: 3 residues within 4Å: Chain B: I.255, L.626, P.694 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.255, B:L.626

2 x CA: CALCIUM ION(Non-covalent)

CA.24: 3 residues within 4Å: Chain A: D.288 Chain B: D.288 Ligands: CA.48 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.288, A:D.288 CA.48: 3 residues within 4Å: Chain A: D.288 Chain B: D.288 Ligands: CA.24 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.288, B:D.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thapper, A. et al., Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase. J.Biol.Inorg.Chem. (2007)

Release Date

2010-02-16

Peptides

Aldehyde oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Aldehyde oxidoreductase

Related Entries With Identical Sequence