SMTL ID : 3inl.2 (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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.40, A:D.109 Water bridges: A:T.39 NA.8: 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.14: 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:Q.196 NA.20: 4 residues within 4Å: Chain D: T.39, V.40, D.109, Q.196 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.39, D:V.40

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

EDO.2: 6 residues within 4Å: Chain A: N.169, F.170, C.301, S.302, F.465 Ligands: BXB.6 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: R.329, V.330, V.331 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: Y.153, R.155 Chain B: S.443, Q.444 Chain D: F.151 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: F.18, Y.101, Y.203 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: F.151 Chain C: N.440, S.443 Chain D: Y.153, R.155 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain B: N.169, F.170, C.301, S.302, C.303, F.465 Ligands: BXB.11 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain B: N.41, T.44, E.46, L.108 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: F.151 Chain C: Y.153, R.155 Chain D: S.443, Q.444 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: N.440, S.443 Chain B: Y.153, R.155 Chain C: F.151 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain C: N.169, F.170, E.268, C.301, S.302, C.303, F.465 Ligands: BXB.19 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain C: F.350, I.373, A.375, D.376, G.378 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain C: N.41, T.44, E.46, I.48, L.108 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain C: D.98, Y.101, Y.203 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain D: N.169, F.170, C.301, S.302, C.303, F.465 Ligands: BXB.24 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain D: N.41, T.44, E.46, V.47, I.48 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain D: F.18, Y.101, Y.203 Ligand excluded by PLIP

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

BXB.6: 13 residues within 4Å: Chain A: V.120, M.124, F.170, L.173, W.177, F.292, F.296, C.301, D.457, V.458, F.459 Chain B: F.150 Ligands: EDO.2 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.170, A:F.296, A:D.457, A:V.458, A:V.458, B:F.150 Hydrogen bonds: A:D.457 pi-Stacking: A:F.459 BXB.11: 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.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.170, B:F.296, 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: 12 residues within 4Å: Chain C: V.120, M.124, F.170, L.173, W.177, F.292, F.296, C.301, D.457, V.458, F.459 Ligands: EDO.15 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.170, C:F.296, C:F.296, C:D.457, C:V.458, C:F.459, C:F.459 Hydrogen bonds: C:D.457 BXB.24: 11 residues within 4Å: Chain D: M.124, F.170, L.173, W.177, F.292, F.296, C.301, D.457, V.458, F.459 Ligands: EDO.21 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.170, D:F.296, D:F.296, D:D.457, D:V.458, D:V.458, D:F.459, D:F.459 Hydrogen bonds: D:D.457

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
E

B
F

C
G

D
H

Aldehyde dehydrogenase, mitochondrial

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