SMTL ID : 2onm.1 (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: 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:V.40, A:Q.196 NA.5: 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:V.404 NA.6: 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:Q.196 NA.11: 6 residues within 4Å: Chain C: N.275, A.290, A.293, G.305, T.308, M.405 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.308 Water bridges: C:T.308 NA.12: 5 residues within 4Å: Chain C: V.40, P.42, D.109, Q.196, V.345 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.40, C:D.109, C:V.345 NA.16: 5 residues within 4Å: Chain D: V.40, P.42, D.109, Q.196, V.345 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.40, D:D.109, D:V.345

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

ADP.2: 18 residues within 4Å: Chain A: I.165, I.166, W.168, K.192, A.194, E.195, G.225, P.226, G.229, A.230, F.243, T.244, G.245, S.246, I.249, V.252, I.253, Q.349 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.166, A:K.192, A:E.195, A:Q.196, A:S.246, A:S.246, A:Q.349 ADP.17: 16 residues within 4Å: Chain D: I.165, I.166, W.168, K.192, E.195, Q.196, G.225, P.226, G.229, A.230, F.243, T.244, G.245, S.246, I.249, I.253 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:I.166, D:K.192, D:E.195, D:Q.196, D:S.246, D:S.246

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

EDO.3: 3 residues within 4Å: Chain A: F.18, Y.101, Y.203 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.203 EDO.8: 7 residues within 4Å: Chain A: Y.153, R.155, V.491 Chain B: N.440, S.443, Q.444 Chain D: F.151 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.443, A:Y.153, A:R.155 EDO.9: 6 residues within 4Å: Chain B: Q.14, N.41, E.46, V.47, I.48, L.108 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.14, B:V.47 EDO.10: 4 residues within 4Å: Chain B: F.18, D.98, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.98 Water bridges: B:D.98 EDO.14: 5 residues within 4Å: Chain C: N.41, T.44, E.46, I.48, L.108 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.44 EDO.15: 3 residues within 4Å: Chain C: D.98, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.98, C:Y.203 EDO.18: 7 residues within 4Å: Chain A: F.151 Chain C: N.440, S.443, Q.444 Chain D: Y.153, R.155, V.491 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.443, D:R.155 EDO.19: 4 residues within 4Å: Chain D: F.18, D.98, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.98 Water bridges: D:D.98

2 x GAI: GUANIDINE(Non-covalent)

GAI.4: 5 residues within 4Å: Chain A: I.146, D.147, 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, A:D.147 Water bridges: B:A.461 GAI.20: 6 residues within 4Å: Chain A: N.440 Chain B: F.151, V.493 Chain C: F.151 Chain D: L.436, N.440 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:N.440, A:N.440, A:N.440, D:N.440 Water bridges: C:Y.153

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

NAD.7: 25 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, L.269, G.270, C.302, Q.349, E.399, F.401 14 PLIP interactions: 14 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:S.246, B:L.269, B:Q.349, B:Q.349 Water bridges: B:E.195, B:Q.196, B:S.246 NAD.13: 27 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 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:P.167 Hydrogen bonds: C:I.166, C:N.169, C:K.192, C:E.195, C:G.245, C:S.246, C:C.302, C:Q.349, C:Q.349, C:E.399, C:E.399 pi-Stacking: C:F.401

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
A

B
B

C
C

D
D

Aldehyde dehydrogenase, mitochondrial precursor

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