SMTL ID : 2onm.3 (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

5 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:T.39, A:V.40, A:D.109 NA.6: 5 residues within 4Å: Chain B: V.40, P.42, D.109, Q.196, V.345 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.109, B:D.109 Water bridges: B:T.39 NA.9: 5 residues within 4Å: Chain C: N.275, A.290, A.293, G.305, T.308 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.305 NA.10: 5 residues within 4Å: Chain C: T.39, V.40, P.42, D.109, Q.196 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.40, C:V.40, C:D.109 NA.13: 4 residues within 4Å: Chain D: T.39, V.40, D.109, Q.196 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.39, D:V.40 Water bridges: D:V.40, D:D.109

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

ADP.2: 18 residues within 4Å: Chain A: I.165, I.166, P.167, 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.166, A:W.168, A:W.168, A:K.192, A:E.195, A:S.246 ADP.7: 17 residues within 4Å: Chain B: I.165, I.166, W.168, K.192, V.193, E.195, Q.196, F.224, G.225, P.226, G.229, A.230, F.243, G.245, S.246, I.249, I.253 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.166, B:K.192, B:E.195, B:Q.196, B:S.246, B:S.246 ADP.11: 18 residues within 4Å: Chain C: I.165, I.166, W.168, K.192, V.193, 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 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:I.166, C:K.192, C:E.195, C:Q.196, C:S.246 Water bridges: C:Q.196, C:Q.349 ADP.14: 16 residues within 4Å: Chain D: 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 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:I.166, D:K.192, D:E.195, D:Q.196, D:S.246, D:S.246, D:S.246 Water bridges: D:Q.349

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

EDO.3: 3 residues within 4Å: Chain A: N.41, T.44, E.46 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.44 EDO.4: 3 residues within 4Å: Chain A: F.18, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.98, A:Y.203 EDO.12: 4 residues within 4Å: Chain C: F.18, D.98, Y.101, Y.203 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.98, C:Y.203 EDO.15: 6 residues within 4Å: Chain A: F.151 Chain C: N.440, S.443 Chain D: Y.153, R.155, V.491 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.155, C:S.443 EDO.16: 3 residues within 4Å: Chain D: F.18, Y.101, Y.203 No protein-ligand interaction detected (PLIP)

2 x GAI: GUANIDINE(Non-covalent)

GAI.5: 4 residues within 4Å: Chain A: D.147, G.148, F.150 Chain B: 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.8: 6 residues within 4Å: Chain A: V.458, F.459 Chain B: I.146, D.147, G.148, F.150 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.147, A:F.459 Water bridges: B:D.147

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
I

B
J

C
K

D
L

Aldehyde dehydrogenase, mitochondrial precursor

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