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

Human Mitochondrial Aldehyde Dehydrogenase complexed with agonist Alda-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 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.7: 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:T.39, B:V.40 NA.13: 4 residues within 4Å: Chain C: T.39, V.40, D.109, Q.196 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.39, C:V.40, C:D.109, C:D.109 NA.18: 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:T.39, D:V.40, D:V.40

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

EDO.2: 8 residues within 4Å: Chain A: N.169, F.170, C.301, C.302, C.303, F.459, F.465 Ligands: BXB.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.169, A:C.302, A:C.303 EDO.3: 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 B, 1 interactions with chain A Hydrogen bonds: B:S.443, A:R.155 EDO.6: 5 residues within 4Å: Chain A: F.151 Chain C: N.440, S.443 Chain D: Y.153, R.155 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.443, D:Y.153, D:R.155 Water bridges: C:S.443 EDO.8: 8 residues within 4Å: Chain B: N.169, F.170, C.301, C.302, C.303, L.427, F.465 Ligands: BXB.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.169, B:C.302, B:C.303 EDO.9: 5 residues within 4Å: Chain A: N.440, S.443 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:R.155, A:S.443 Water bridges: B:Y.153 EDO.12: 6 residues within 4Å: Chain B: F.151 Chain C: Y.153, R.155 Chain D: N.440, S.443, Q.444 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.443, C:R.155 EDO.14: 6 residues within 4Å: Chain B: H.140, G.141, K.142 Chain C: H.140, G.141, K.142 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:H.140, C:K.142, B:H.140, B:K.142 Water bridges: C:H.140, B:H.140 EDO.17: 6 residues within 4Å: Chain A: H.140, G.141, K.142 Chain D: H.140, G.141, K.142 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:H.140, D:K.142, A:H.140, A:K.142 EDO.19: 7 residues within 4Å: Chain D: N.169, F.170, C.301, C.302, C.303, F.465 Ligands: BXB.21 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.169, D:C.302

4 x GAI: GUANIDINE(Non-covalent)

GAI.4: 6 residues within 4Å: Chain A: F.70, E.157, P.158, V.159 Chain B: Q.447, Y.468 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.158, A:P.158 Water bridges: A:R.77 Salt bridges: A:E.157 GAI.10: 5 residues within 4Å: Chain A: Y.468 Chain B: F.70, E.157, P.158, V.159 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Y.468, B:P.158 Water bridges: A:Q.447, B:R.77, B:E.157, B:V.159 Salt bridges: B:E.157 GAI.15: 5 residues within 4Å: Chain C: E.157, P.158, V.159, G.160 Chain D: Y.468 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:P.158, C:P.158 Water bridges: C:R.77, C:E.157, C:V.159, C:E.487, D:Q.447 Salt bridges: C:E.157 GAI.20: 4 residues within 4Å: Chain C: Y.468 Chain D: E.157, P.158, V.159 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:P.158, D:P.158 Water bridges: D:R.77, D:E.157 Salt bridges: D:E.157

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

BXB.5: 10 residues within 4Å: Chain A: M.124, F.170, L.173, 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.11: 11 residues within 4Å: Chain B: V.120, M.124, F.170, L.173, F.292, F.296, C.301, D.457, V.458, F.459 Ligands: EDO.8 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.16: 10 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 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.21: 10 residues within 4Å: Chain D: M.124, F.170, L.173, F.292, F.296, C.301, D.457, V.458, F.459 Ligands: EDO.19 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
A

B
B

C
C

D
D

Aldehyde dehydrogenase, mitochondrial

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