SMTL ID : 1o01.1 (1 other biounit)

Human mitochondrial aldehyde dehydrogenase complexed with crotonaldehyde, NAD(H) and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: NAD.4 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: NAD.9 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: NAD.16 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Ligands: NAD.23 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:Q.196 Water bridges: A:T.39 NA.6: 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 Water bridges: B:T.39 NA.11: 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.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:V.40, D:D.109, D:Q.196

4 x GAI: GUANIDINE(Non-covalent)

GAI.3: 6 residues within 4Å: Chain A: F.70, E.157, P.158, V.159, G.160 Chain B: Y.468 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.158, A:P.158 Water bridges: A:V.159, B:Q.447 Salt bridges: A:E.157 GAI.8: 5 residues within 4Å: Chain A: Y.468 Chain B: F.70, E.157, P.158, V.159 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.468, B:P.158 Water bridges: A:Q.447, B:E.157, B:V.159 Salt bridges: B:E.157 GAI.13: 6 residues within 4Å: Chain C: F.70, E.157, P.158, V.159, G.160 Chain D: Y.468 7 PLIP interactions: 6 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, D:Q.447 Salt bridges: C:E.157 GAI.20: 6 residues within 4Å: Chain C: 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

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

NAD.4: 28 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, 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.1 18 PLIP interactions: 18 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:G.245, A:S.246, A:S.246, A:Q.349, A:K.352 Water bridges: A:W.168, A:E.195, A:G.225, A:E.399, A:I.400 pi-Stacking: A:F.401 NAD.9: 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, G.270, C.302, Q.349, E.399, F.401 Ligands: MG.5 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:P.167 Hydrogen bonds: B:I.166, B:N.169, B:K.192, B:E.195, B:Q.196, B:G.245, B:G.245, B:S.246, B:S.246, B:Q.349, B:Q.349, B:K.352 Water bridges: B:W.168, B:E.195, B:K.352, B:E.399 pi-Stacking: B:F.401 NAD.16: 30 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.10, CRD.12 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:P.167 Hydrogen bonds: C:I.166, C:N.169, C:K.192, C:E.195, C:Q.196, C:G.245, C:G.245, C:S.246, C:S.246, C:Q.349, C:Q.349, C:K.352, C:E.399 Water bridges: C:W.168, C:E.195, C:G.225, C:E.399, C:I.400 pi-Stacking: C:F.401 NAD.23: 30 residues within 4Å: Chain D: I.165, I.166, P.167, W.168, N.169, K.192, V.193, 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.17, CRD.19 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:P.167 Hydrogen bonds: D:I.166, D:N.169, D:K.192, D:E.195, D:Q.196, D:G.245, D:G.245, D:S.246, D:S.246, D:Q.349, D:K.352, D:E.399 Water bridges: D:W.168, D:E.195, D:G.225, D:K.352, D:E.399, D:I.400 pi-Stacking: D:F.401

3 x CRD: (2E)-BUT-2-ENAL(Non-covalent)

CRD.7: 4 residues within 4Å: Chain B: F.170, C.302, C.303, F.459 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.459, B:F.459 Hydrogen bonds: B:N.169, B:C.302 CRD.12: 4 residues within 4Å: Chain C: F.170, C.302, F.459 Ligands: NAD.16 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.170, C:F.170, C:F.459 CRD.19: 6 residues within 4Å: Chain D: N.169, F.170, C.302, C.303, F.459 Ligands: NAD.23 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.170, D:F.170, D:F.459 Hydrogen bonds: D:N.169, D:C.302

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

EDO.14: 5 residues within 4Å: Chain A: N.440, S.443 Chain B: Y.153, R.155 Chain C: F.151 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.153, B:R.155, A:S.443 Water bridges: A:S.443 EDO.15: 5 residues within 4Å: Chain B: F.151 Chain C: Y.153, R.155 Chain D: N.440, S.443 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.443, C:R.155 Water bridges: C:Y.153 EDO.21: 6 residues within 4Å: Chain A: Y.153, R.155 Chain B: N.440, S.443, Q.444 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.22: 6 residues within 4Å: Chain A: F.151 Chain C: N.440, S.443 Chain D: Y.153, R.155, V.491 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.155, C:S.443

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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