SMTL ID : 1o04.1 (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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.39, A:V.40, A:D.109 Water bridges: A:T.39 NA.10: 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:V.40 Water bridges: B:T.39 NA.19: 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:T.39, C:V.40, C:D.109 NA.30: 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

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

MG.2: 1 residues within 4Å: Ligands: NAD.3 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: NAD.12 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Ligands: NAD.21 No protein-ligand interaction detected (PLIP) MG.31: 1 residues within 4Å: Ligands: NAD.32 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 19 PLIP interactions: 19 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:E.268, A:L.269, A:S.302, A:E.399 Water bridges: A:W.168, A:N.169, A:Q.196, A:Q.196, A:Q.196, A:G.225, A:T.247, A:E.399 NAD.12: 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.11 17 PLIP interactions: 17 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:L.269, B:S.302, B:E.399 Water bridges: B:Q.196, B:Q.196, B:Q.196, B:G.225, B:S.246, B:T.247, B:E.399 NAD.21: 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.20 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:P.167, C:T.244 Hydrogen bonds: C:I.166, C:W.168, C:K.192, C:E.195, C:S.246, C:L.269, C:S.302, C:E.399 Water bridges: C:Q.196, C:Q.196, C:Q.196, C:Q.196, C:Q.196, C:Q.196, C:G.225, C:S.246, C:S.246, C:T.247, C:E.399, C:E.399 NAD.32: 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.31 19 PLIP interactions: 19 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:E.268, D:L.269, D:S.302, D:E.399 Water bridges: D:Q.196, D:Q.196, D:Q.196, D:G.225, D:S.246, D:T.247, D:E.399, D:E.399

9 x GAI: GUANIDINE(Non-covalent)

GAI.4: 5 residues within 4Å: Chain A: F.70, E.157, P.158, V.159 Chain B: 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.5: 6 residues within 4Å: Chain A: I.146, D.147, G.148, F.150 Chain B: V.458, F.459 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.147, B:F.459, B:F.459 Water bridges: A:D.147 GAI.13: 6 residues within 4Å: Chain A: Q.447, Y.468 Chain B: F.70, E.157, P.158, V.159 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.158 Water bridges: B:R.77, B:E.157, B:V.159 Salt bridges: B:E.157 GAI.14: 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.22: 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.23: 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, C:D.147, D:F.459, D:F.459 Water bridges: C:D.147 GAI.24: 6 residues within 4Å: Chain C: F.350, I.373, A.375, D.376, G.378 Ligands: EDO.29 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.375, C:D.376 Water bridges: C:G.378 GAI.33: 5 residues within 4Å: Chain C: 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.34: 6 residues within 4Å: Chain C: V.458, F.459 Chain D: I.146, D.147, G.148, F.150 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.147, D:D.147, C:F.459 Water bridges: D:D.147, D:D.147, 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: 3 residues within 4Å: Chain A: F.18, Y.101, Y.203 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Y.441, Q.444, A.445 Chain B: L.72 Chain C: Q.497 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: 7 residues within 4Å: Chain B: Q.14, N.41, T.44, E.46, V.47, I.48, L.108 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: R.97, D.98, R.99, T.100, Y.101 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: L.72 Chain B: Y.441, Q.444, A.445 Chain D: Q.497 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: F.151 Chain C: Y.153, R.155 Chain D: N.440, S.443 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain C: N.41, T.44, E.46, V.47, I.48, L.108 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain C: F.18, D.98, Y.101, Y.203 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: Q.497 Chain C: Y.441, Q.444, A.445 Chain D: L.72 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain C: E.347, F.350 Ligands: GAI.24 Ligand excluded by PLIP EDO.35: 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.36: 4 residues within 4Å: Chain D: N.41, T.44, E.46, L.108 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain D: E.414, V.417, Y.441 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
A

B
B

C
C

D
D

Aldehyde dehydrogenase, mitochondrial precursor

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