SMTL ID : 1o04.2 (1 other biounit)

Cys302Ser mutant of human mitochondrial aldehyde dehydrogenase complexed with NAD+ and Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 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:Q.196 Water bridges: A:T.39 NA.9: 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:T.39, B:V.40 Water bridges: B:T.39 NA.21: 4 residues within 4Å: Chain C: T.39, V.40, D.109, Q.196 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.40, C:D.109, C:D.109 NA.29: 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:V.40, D:D.109

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

MG.2: 1 residues within 4Å: Ligands: NAD.3 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: NAD.11 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Ligands: NAD.23 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Ligands: NAD.31 No protein-ligand interaction detected (PLIP)

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 30 residues within 4Å: Chain A: I.165, I.166, P.167, W.168, N.169, M.174, W.177, 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, E.268, L.269, G.270, S.302, E.399, F.401, L.427, F.465 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.167, A:T.244 Hydrogen bonds: A:I.166, A:W.168, A:K.192, A:E.195, A:S.246, A:L.269, A:S.302, A:E.399 Water bridges: A:W.168, A:Q.196, A:Q.196, A:Q.196, A:G.225, A:S.246, A:T.247, A:E.399 NAD.11: 30 residues within 4Å: Chain B: I.165, I.166, P.167, W.168, N.169, M.174, W.177, 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, E.268, L.269, G.270, S.302, E.399, F.401, L.427, F.465 Ligands: MG.10 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:P.167, B:T.244 Hydrogen bonds: B:I.166, B:W.168, B:K.192, B:E.195, B:S.246, B:E.268, B:L.269, B:S.302, B:E.399 Water bridges: B:W.168, B:Q.196, B:Q.196, B:Q.196, B:G.225, B:S.246, B:T.247, B:E.399 NAD.23: 30 residues within 4Å: Chain C: I.165, I.166, P.167, W.168, N.169, M.174, W.177, 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, E.268, L.269, G.270, S.302, E.399, F.401, L.427, F.465 Ligands: MG.22 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:P.167, C:T.244 Hydrogen bonds: C:I.166, C:I.166, C:W.168, C:K.192, C:E.195, C:S.246, C:E.268, C:L.269, C:S.302, C:E.399 Water bridges: C:Q.196, C:Q.196, C:Q.196, C:Q.196, C:G.225, C:S.246, C:T.247, C:E.399, C:E.399 NAD.31: 30 residues within 4Å: Chain D: I.165, I.166, P.167, W.168, N.169, M.174, W.177, 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, E.268, L.269, G.270, S.302, E.399, F.401, L.427, F.465 Ligands: MG.30 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:P.167, D:T.244 Hydrogen bonds: D:I.166, D:W.168, D:K.192, D:E.195, D:S.246, D:L.269, D:S.302, D:E.399 Water bridges: D:N.169, D:Q.196, D:Q.196, D:Q.196, D:Q.196, D:G.225, D:T.247

9 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 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.158 Water bridges: A:R.77, A:E.157, A:V.159, B:Q.447, B:Y.468 Salt bridges: A:E.157 GAI.5: 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.12: 6 residues within 4Å: Chain A: Q.447, Y.468 Chain B: F.70, E.157, P.158, V.159 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.158, B:P.158 Water bridges: B:R.77, B:E.157, B:V.159 Salt bridges: B:E.157 GAI.13: 6 residues within 4Å: Chain A: V.458, F.459 Chain B: I.146, D.147, G.148, F.150 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.459, A:F.459, A:F.459, B:D.147 Water bridges: B:D.147 GAI.14: 6 residues within 4Å: Chain B: F.350, I.373, A.375, D.376, G.378 Ligands: EDO.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.375 Water bridges: B:D.376 GAI.24: 5 residues within 4Å: Chain C: F.70, E.157, P.158, V.159 Chain D: Y.468 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:P.158, C:P.158 Water bridges: C:R.77, C:E.157, C:V.159 Salt bridges: C:E.157 GAI.25: 6 residues within 4Å: Chain C: I.146, D.147, G.148, F.150 Chain D: V.458, F.459 6 PLIP interactions: 4 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, C:D.147 GAI.32: 6 residues within 4Å: Chain C: Q.447, Y.468 Chain D: F.70, 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 GAI.33: 6 residues within 4Å: Chain C: V.458, F.459 Chain D: I.146, D.147, G.148, F.150 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.147, D:D.147, C:F.459, C:F.459, C:F.459 Water bridges: D:D.147, D:D.147

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

EDO.6: 5 residues within 4Å: Chain A: Y.153, R.155 Chain B: N.440, S.443 Chain D: F.151 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: Q.14, N.41, T.44, E.46, V.47, I.48, L.108 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: F.18, D.98, Y.101, Y.203 Ligand excluded by PLIP EDO.15: 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.16: 6 residues within 4Å: Chain B: N.41, T.44, E.46, V.47, I.48, L.108 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: F.18, Y.101, Y.203 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: L.72 Chain B: Y.441, Q.444, A.445 Chain D: Q.497, N.499 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: A.68, Q.71, S.74 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: E.347, F.350 Ligands: GAI.14 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: F.151 Chain C: Y.153, R.155 Chain D: N.440, S.443, Q.444 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain C: N.41, T.44, E.46, V.47, I.48, L.108 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain C: F.18, Y.101, Y.203 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain A: F.151 Chain C: N.440, S.443, Q.444 Chain D: Y.153, R.155 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain D: N.41, T.44, E.46, I.48, L.108 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain D: F.18, Y.101, Y.203 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain B: Q.497 Chain C: L.72 Chain D: Y.441, Q.444, A.445 Ligand excluded by PLIP

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, mitochondrial precursor: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Aldehyde dehydrogenase, mitochondrial precursor

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