SMTL ID : 2onp.1 (1 other biounit)

Arg475Gln Mutant of Human Mitochondrial Aldehyde Dehydrogenase, complexed with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 1 residues within 4Å: Ligands: NAD.3 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: NAD.15 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Ligands: NAD.26 No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Ligands: NAD.39 No protein-ligand interaction detected (PLIP)

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

NA.2: 4 residues within 4Å: Chain A: T.39, V.40, D.109, Q.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.39, A:V.40 NA.14: 4 residues within 4Å: Chain B: T.39, V.40, D.109, Q.196 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.39, B:V.40 Water bridges: B:T.39 NA.25: 4 residues within 4Å: Chain C: T.39, V.40, D.109, Q.196 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.40, C:V.40 NA.38: 4 residues within 4Å: Chain D: T.39, V.40, D.109, Q.196 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.40, D:D.109, D:Q.196

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 28 residues within 4Å: Chain A: I.165, I.166, P.167, W.168, N.169, K.192, A.194, E.195, Q.196, G.225, P.226, G.229, A.230, F.243, T.244, G.245, S.246, I.249, I.253, E.268, L.269, G.270, C.302, Q.349, K.352, E.399, F.401 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.167 Hydrogen bonds: A:I.166, A:N.169, A:K.192, A:E.195, A:G.245, A:G.245, A:S.246, A:S.246, A:Q.349, A:K.352 Water bridges: A:E.195, A:Q.196, A:G.225, A:K.352, A:K.352 pi-Stacking: A:F.401 NAD.15: 28 residues within 4Å: Chain B: I.165, I.166, P.167, W.168, N.169, K.192, A.194, E.195, Q.196, F.224, G.225, P.226, G.229, A.230, F.243, G.245, S.246, I.249, I.253, E.268, L.269, G.270, C.302, Q.349, K.352, E.399, F.401 Ligands: MG.13 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.167, B:F.401, B:F.401 Hydrogen bonds: B:I.166, B:N.169, B:K.192, B:E.195, B:G.245, B:G.245, B:S.246, B:S.246, B:Q.349, B:Q.349, B:K.352 Water bridges: B:E.399, B:I.400 NAD.26: 28 residues within 4Å: Chain C: I.165, I.166, P.167, W.168, N.169, K.192, A.194, E.195, Q.196, G.225, P.226, G.229, A.230, F.243, T.244, G.245, S.246, I.249, I.253, E.268, L.269, G.270, C.302, Q.349, K.352, E.399, F.401 Ligands: MG.24 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:P.167, C:F.401, C:F.401 Hydrogen bonds: C:I.166, C:N.169, C:K.192, C:E.195, C:G.245, C:G.245, C:S.246, C:S.246, C:Q.349, C:K.352, C:E.399 Water bridges: C:W.168, C:E.195, C:Q.196, C:G.225, C:E.399, C:I.400 NAD.39: 29 residues within 4Å: Chain D: I.165, I.166, P.167, W.168, N.169, K.192, V.193, A.194, E.195, Q.196, G.225, P.226, G.229, A.230, F.243, T.244, G.245, S.246, I.249, V.252, I.253, E.268, L.269, C.302, Q.349, K.352, E.399, F.401 Ligands: MG.37 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:P.167, D:F.401, D:F.401 Hydrogen bonds: D:I.166, D:N.169, D:K.192, D:E.195, D:G.245, D:S.246, D:S.246, D:C.302, D:Q.349, D:K.352, D:E.399 Water bridges: D:W.168, D:Q.196, D:K.352, D:K.352

19 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: Y.153, R.155 Chain B: N.440, S.443 Chain D: F.151 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: N.41, T.44, E.46, V.47, I.48, L.108 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: F.18, Y.101, Y.203 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: Y.441, Q.444, A.445 Chain B: L.72 Chain C: Q.497 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: A.68, Q.71 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: N.440, S.443 Chain B: Y.153, R.155, V.491 Chain C: F.151 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: Q.14, N.41, T.44, E.46, I.48, L.108 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: L.72 Chain B: Y.441, Q.444, A.445 Chain D: Q.497 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: A.68, Q.71, S.74 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: E.347, F.350, K.351 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: F.151 Chain C: Y.153, R.155 Chain D: N.440, S.443, Q.444 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain C: N.41, T.44, E.46, V.47, I.48, L.108 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain C: F.18, Y.101, Y.203 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain A: Q.497 Chain C: Y.441, Q.444, A.445 Chain D: L.72 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain C: A.68, Q.71, S.74 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain C: E.347, F.350, Y.379 Ligands: GAI.35 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain A: F.151 Chain C: S.443 Chain D: Y.153, R.155, V.491 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain D: N.41, T.44, E.46, I.48 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain D: F.18, D.98, Y.101, Y.203 Ligand excluded by PLIP

15 x GAI: GUANIDINE(Non-covalent)

GAI.9: 6 residues within 4Å: Chain A: F.70, E.157, P.158, V.159 Chain B: Q.447, Y.468 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.158, A:P.158, B:Y.468 Water bridges: A:R.77, A:E.157 Salt bridges: A:E.157 GAI.10: 6 residues within 4Å: Chain A: I.146, D.147, G.148, F.150 Chain B: V.458, F.459 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.459, B:F.459, A:D.147 Water bridges: B:F.459, A:D.147 GAI.11: 5 residues within 4Å: Chain A: F.350, I.373, A.375, D.376, G.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.375, A:G.378 GAI.12: 6 residues within 4Å: Chain A: G.467, Y.468, K.469, G.472 Chain B: R.264, E.487 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.467, A:K.469, A:G.472 Salt bridges: B:E.487 GAI.21: 4 residues within 4Å: Chain A: Y.468 Chain B: E.157, P.158, V.159 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.158, B:P.158 Water bridges: B:E.157 Salt bridges: B:E.157 GAI.22: 6 residues within 4Å: Chain A: V.458, F.459 Chain B: I.146, D.147, G.148, F.150 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.147, A:F.459, A:F.459, A:F.459 Water bridges: B:D.147 GAI.23: 6 residues within 4Å: Chain A: R.264, E.487 Chain B: G.467, Y.468, K.469, G.472 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:E.487 Hydrogen bonds: B:K.469, B:G.472, B:G.472 GAI.33: 4 residues within 4Å: Chain C: E.157, P.158, V.159 Chain D: Y.468 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:P.158, C:P.158 Water bridges: C:R.77, C:E.487 Salt bridges: C:E.157 GAI.34: 5 residues within 4Å: Chain C: I.146, D.147, G.148, F.150 Chain D: F.459 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.147, D:F.459, D:F.459 Water bridges: C:D.147, D:F.459 GAI.35: 6 residues within 4Å: Chain C: F.350, I.373, A.375, D.376, G.378 Ligands: EDO.32 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.375, C:G.378 Water bridges: C:A.375 GAI.36: 6 residues within 4Å: Chain C: G.467, Y.468, K.469, G.472 Chain D: R.264, E.487 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.467, C:G.472 Water bridges: D:E.487 Salt bridges: D:E.487 GAI.43: 5 residues within 4Å: Chain C: Q.447, Y.468 Chain D: E.157, P.158, V.159 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:P.158, D:P.158 Water bridges: D:R.77, D:E.157 Salt bridges: D:E.157 GAI.44: 5 residues within 4Å: Chain C: V.458, F.459 Chain D: I.146, D.147, F.150 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:F.459, C:F.459, C:F.459, D:D.147 Water bridges: D:D.147, D:D.147 GAI.45: 6 residues within 4Å: Chain D: F.350, I.373, A.375, D.376, R.377, G.378 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.378 GAI.46: 6 residues within 4Å: Chain C: R.264, E.487 Chain D: G.467, Y.468, K.469, G.472 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Water bridges: C:D.239, C:E.487 Salt bridges: C:E.487 Hydrogen bonds: D:G.472, D:G.472

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larson, H.N. et al., Structural and functional consequences of coenzyme binding to the inactive asian variant of mitochondrial aldehyde dehydrogenase: roles of residues 475 and 487. J.Biol.Chem. (2007)

Release Date

2007-03-06

Peptides

Aldehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Aldehyde dehydrogenase

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