SMTL ID : 1o02.1 (1 other biounit)

Human mitochondrial aldehyde dehydrogenase complexed with NADH in the presence of Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 1 residues within 4Å: Ligands: NAI.6 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: NAI.12 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: NAI.18 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Ligands: NAI.24 No protein-ligand interaction detected (PLIP)

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.40, B:Q.196 Water bridges: B:T.39 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: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, D:Q.196

8 x GAI: GUANIDINE(Non-covalent)

GAI.3: 7 residues within 4Å: Chain A: F.70, E.157, P.158, V.159, G.160 Chain B: Q.447, Y.468 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.158, A:P.158 Water bridges: A:R.77, A:V.159 Salt bridges: A:E.157 GAI.4: 5 residues within 4Å: Chain A: I.146, D.147, F.150 Chain B: V.458, F.459 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.459, B:F.459, A:D.147, A:D.147 GAI.9: 6 residues within 4Å: Chain A: Q.447, Y.468 Chain B: F.70, E.157, P.158, V.159 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:P.158 Water bridges: B:R.77, B:V.159, A:Y.468, A:Y.468 Salt bridges: B:E.157 GAI.10: 6 residues within 4Å: Chain A: V.458, F.459 Chain B: I.146, D.147, G.148, F.150 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.147, B:D.147, A:F.459 Water bridges: B:D.147 GAI.15: 5 residues within 4Å: Chain C: F.70, E.157, P.158, V.159 Chain D: Y.468 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain C Water bridges: D:Q.447, C:R.77, C:E.157, C:V.159 Hydrogen bonds: C:P.158, C:P.158 Salt bridges: C:E.157 GAI.16: 6 residues within 4Å: Chain C: I.146, D.147, G.148, F.150 Chain D: V.458, F.459 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.147, C:D.147, D:F.459, D:F.459 Water bridges: C:D.147 GAI.21: 7 residues within 4Å: Chain C: Q.447, Y.468 Chain D: F.70, E.157, P.158, V.159, G.160 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 GAI.22: 5 residues within 4Å: Chain C: V.458, F.459 Chain D: I.146, D.147, F.150 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:F.459, D:D.147, D:D.147 Water bridges: D:D.147

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

EDO.5: 5 residues within 4Å: Chain A: Y.153, R.155 Chain B: N.440, S.443 Chain D: F.151 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.155, B:S.443 Water bridges: A:Y.153 EDO.11: 5 residues within 4Å: Chain A: N.440, S.443 Chain B: Y.153, R.155 Chain C: F.151 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.443, B:Y.153, B:R.155 EDO.17: 5 residues within 4Å: Chain B: F.151 Chain C: Y.153, R.155 Chain D: N.440, S.443 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.443, C:R.155 EDO.23: 5 residues within 4Å: Chain A: F.151 Chain C: N.440, S.443 Chain D: Y.153, R.155 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.443, D:R.155 Water bridges: D:Y.153

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.6: 27 residues within 4Å: Chain A: 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, G.245, S.246, I.249, I.253, E.268, L.269, G.270, C.302, Q.349, K.352, E.399, F.401 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.167 Hydrogen bonds: A:I.166, A:N.169, A:K.192, A:E.195, A:Q.196, A:G.245, A:S.246, A:S.246, A:E.268, A:Q.349, A:Q.349, A:K.352 Water bridges: A:G.225, A:E.399, A:I.400 pi-Stacking: A:F.401 NAI.12: 27 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, E.268, L.269, C.302, Q.349, K.352, E.399, F.401 Ligands: MG.7 19 PLIP interactions: 19 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:Q.196, B:G.245, B:S.246, B:S.246, B:E.268, B:C.302, B:Q.349, B:Q.349, B:K.352 Water bridges: B:G.225, B:E.399, B:I.400 NAI.18: 29 residues within 4Å: Chain C: I.165, I.166, P.167, W.168, N.169, K.192, A.194, E.195, Q.196, F.224, 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 Ligands: MG.13 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:P.167, C:W.168, C:F.401, C:F.401 Hydrogen bonds: C:I.166, C:N.169, C:K.192, C:E.195, C:Q.196, C:G.245, C:S.246, C:S.246, C:E.268, C:C.302, C:Q.349, C:Q.349, C:K.352, C:E.399 Water bridges: C:G.225, C:E.399, C:I.400 NAI.24: 28 residues within 4Å: Chain D: 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 Ligands: MG.19 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:P.167, D:W.168, D:F.401, D:F.401 Hydrogen bonds: D:I.166, D:N.169, D:K.192, D:E.195, D:Q.196, D:G.245, D:S.246, D:S.246, D:E.268, D:C.302, D:Q.349, D:K.352, D:E.399 Water bridges: D:K.352, D:E.399

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perez-Miller, S.J. et al., Coenzyme isomerization is integral to catalysis in aldehyde dehydrogenase. Biochemistry (2003)

Release Date

2003-06-24

Peptides

Aldehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Aldehyde dehydrogenase

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