SMTL ID : 2onm.2 (2 other biounits)

Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: T.39, V.40, P.42, D.109, Q.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.40, A:D.109, A:D.109 NA.8: 4 residues within 4Å: Chain B: G.299, A.304, F.401, G.402 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.299, B:F.401, B:G.402 Water bridges: B:I.400, B:I.400 NA.9: 4 residues within 4Å: Chain B: T.39, V.40, D.109, Q.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.40, B:D.109 NA.15: 5 residues within 4Å: Chain C: N.275, A.290, A.293, G.305, T.308 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.308 Water bridges: C:T.308 NA.16: 4 residues within 4Å: Chain C: T.39, V.40, D.109, Q.196 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.39, C:V.40 Water bridges: C:T.39 NA.22: 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:V.40, D:D.109

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 17 residues within 4Å: Chain A: I.165, I.166, W.168, K.192, A.194, E.195, Q.196, G.225, P.226, G.229, A.230, F.243, G.245, S.246, I.249, I.253, Q.349 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.166, A:K.192, A:E.195, A:S.246, A:S.246 Water bridges: A:Q.196, A:Q.196, A:Q.349

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

EDO.3: 5 residues within 4Å: Chain A: Y.153, R.155 Chain B: N.440, S.443 Chain D: F.151 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.155, B:S.443 Water bridges: A:Y.153 EDO.4: 5 residues within 4Å: Chain A: N.41, T.44, E.46, I.48, L.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.46, A:E.46 EDO.5: 3 residues within 4Å: Chain A: F.18, Y.101, Y.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.98, A:Y.203 Water bridges: A:D.98 EDO.11: 6 residues within 4Å: Chain A: N.440, S.443 Chain B: Y.153, R.155, V.491 Chain C: F.151 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.153, B:R.155, A:S.443 EDO.12: 7 residues within 4Å: Chain B: Q.14, N.41, T.44, E.46, V.47, I.48, L.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.14 EDO.13: 3 residues within 4Å: Chain B: F.18, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.203 Water bridges: B:R.97 EDO.14: 5 residues within 4Å: Chain B: F.151 Chain C: Y.153, R.155 Chain D: N.440, S.443 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.443, C:R.155 EDO.18: 6 residues within 4Å: Chain C: Q.14, N.41, T.44, E.46, I.48, L.108 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.46, C:E.46 Water bridges: C:Q.14, C:Q.14 EDO.19: 2 residues within 4Å: Chain C: Y.101, Y.203 No protein-ligand interaction detected (PLIP) EDO.24: 5 residues within 4Å: Chain A: F.151 Chain C: N.440, S.443 Chain D: Y.153, R.155 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.155, C:S.443 Water bridges: D:Y.153 EDO.25: 4 residues within 4Å: Chain D: N.41, T.44, E.46, L.108 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.44 EDO.26: 4 residues within 4Å: Chain D: F.18, D.98, Y.101, Y.203 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.98

5 x GAI: GUANIDINE(Non-covalent)

GAI.6: 6 residues within 4Å: Chain A: I.146, D.147, G.148, F.150 Chain B: V.458, F.459 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.147, B:F.459 Water bridges: B:F.459 GAI.7: 6 residues within 4Å: Chain A: L.436, N.440 Chain C: Y.153, V.493 Chain D: L.436, N.440 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: A:N.440, A:N.440, A:N.440, C:Y.153, D:N.440, D:N.440 GAI.20: 6 residues within 4Å: Chain C: I.146, D.147, F.150 Chain D: V.458, F.459, G.460 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:F.459, D:F.459, C:D.147, C:D.147 GAI.21: 4 residues within 4Å: Chain A: F.151 Chain B: N.440 Chain C: N.440 Chain D: V.493 7 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: B:N.440, C:N.440, C:N.440 Water bridges: D:Y.153, D:Y.153, A:Y.153, A:Y.153 GAI.27: 5 residues within 4Å: Chain C: V.458, F.459 Chain D: I.146, D.147, F.150 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.147, D:D.147, C:F.459, C:F.459

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

NAD.10: 27 residues within 4Å: Chain B: 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 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:S.246, B:Q.349, B:Q.349, B:K.352 Water bridges: B:W.168, B:Q.196, B:E.399, B:I.400 NAD.17: 26 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, L.269, G.270, C.302, Q.349, K.352, E.399, F.401 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:P.167 Hydrogen bonds: C:I.166, C:N.169, C:K.192, C:E.195, C:S.246, C:L.269, C:Q.349, C:Q.349, C:E.399, C:E.399 Water bridges: C:G.225, C:K.352 pi-Stacking: C:F.401 NAD.23: 27 residues within 4Å: Chain D: I.165, I.166, P.167, W.168, N.169, K.192, E.195, Q.196, F.224, G.225, P.226, G.229, A.230, F.243, T.244, G.245, S.246, I.249, V.252, I.253, L.269, G.270, C.302, Q.349, K.352, E.399, F.401 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:P.167, D:F.401 Hydrogen bonds: D:I.166, D:N.169, D:K.192, D:E.195, D:S.246, D:Q.349, D:Q.349, D:K.352, D:E.399 Water bridges: D:W.168, D:E.195

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, mitochondrial precursor: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Aldehyde dehydrogenase, mitochondrial precursor

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