SMTL ID : 3inl.1 (1 other biounit)

Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with agonist Alda-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-tetramer

Ligands

4 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:D.109 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:Q.196 NA.15: 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:T.39, C:V.40 NA.20: 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 Water bridges: D:T.39

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

EDO.2: 7 residues within 4Å: Chain A: N.169, F.170, C.301, S.302, C.303, F.465 Ligands: BXB.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.169, A:S.302, A:C.303 Water bridges: A:N.169 EDO.3: 6 residues within 4Å: Chain A: L.436, N.440 Chain B: F.151 Chain C: F.151 Chain D: L.436, N.440 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.440, D:N.440 EDO.4: 3 residues within 4Å: Chain A: L.367, C.369, G.370 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.367 Water bridges: A:G.370 EDO.5: 6 residues within 4Å: Chain A: Y.153, R.155 Chain B: N.440, S.443, Q.444 Chain D: F.151 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.155, B:S.443 EDO.6: 4 residues within 4Å: Chain A: N.41, T.44, E.46, L.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.41 Water bridges: A:Q.14, A:Q.14 EDO.7: 4 residues within 4Å: Chain A: F.18, D.98, Y.101, Y.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.98 Water bridges: A:R.97, A:D.98, A:Y.203 EDO.10: 7 residues within 4Å: Chain B: N.169, F.170, C.301, S.302, C.303, F.465 Ligands: BXB.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.169, B:S.302, B:C.303 EDO.11: 4 residues within 4Å: Chain B: K.327, C.369, G.370, Q.382 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.370 Water bridges: B:G.370 EDO.12: 6 residues within 4Å: Chain A: N.440, S.443, Q.444 Chain B: Y.153, R.155 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.13: 6 residues within 4Å: Chain B: N.41, T.44, E.46, V.47, I.48, L.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.44 EDO.16: 7 residues within 4Å: Chain C: N.169, F.170, C.301, S.302, C.303, F.459 Ligands: BXB.19 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.169, C:S.302 EDO.17: 5 residues within 4Å: Chain B: F.151 Chain C: Y.153, R.155 Chain D: N.440, S.443 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.443, C:R.155 Water bridges: D:S.443 EDO.18: 5 residues within 4Å: Chain C: N.41, T.44, E.46, I.48, L.108 No protein-ligand interaction detected (PLIP) EDO.21: 8 residues within 4Å: Chain D: N.169, F.170, E.268, C.301, S.302, C.303, F.465 Ligands: BXB.23 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.169, D:E.268, D:S.302, D:C.303 EDO.22: 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:Y.153, D:R.155, C:S.443

4 x BXB: N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide(Non-covalent)

BXB.8: 11 residues within 4Å: Chain A: M.124, F.170, L.173, W.177, F.292, F.296, C.301, D.457, V.458, F.459 Ligands: EDO.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.170, A:F.296, A:F.296, A:D.457, A:V.458, A:V.458, A:F.459, A:F.459 Hydrogen bonds: A:D.457 BXB.14: 12 residues within 4Å: Chain B: V.120, M.124, F.170, L.173, W.177, F.292, F.296, C.301, D.457, V.458, F.459 Ligands: EDO.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.170, B:F.296, B:D.457, B:V.458, B:V.458, B:F.459, B:F.459 Hydrogen bonds: B:D.457 BXB.19: 11 residues within 4Å: Chain C: M.124, F.170, L.173, W.177, F.292, F.296, C.301, D.457, V.458, F.459 Ligands: EDO.16 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.170, C:F.296, C:F.296, C:D.457, C:V.458, C:V.458, C:F.459, C:F.459 Hydrogen bonds: C:D.457 BXB.23: 10 residues within 4Å: Chain D: M.124, F.170, L.173, W.177, F.292, F.296, D.457, V.458, F.459 Ligands: EDO.21 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.296, D:F.296, D:D.457, D:V.458 Hydrogen bonds: D:D.457 pi-Stacking: D:F.459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perez-Miller, S. et al., Alda-1 is an agonist and chemical chaperone for the common human aldehyde dehydrogenase 2 variant. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-01-12

Peptides

Aldehyde dehydrogenase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Aldehyde dehydrogenase, mitochondrial

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