SMTL ID : 4fqf.1

Crystal structure of a thionitrate intermediate of human aldehyde dehydrogenase-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-tetramer

Ligands

4 x 2NO: NITROGEN DIOXIDE(Covalent)

2NO.1: 5 residues within 4Å: Chain A: N.169, F.170, C.301, C.302 Ligands: NAD.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.302 2NO.8: 5 residues within 4Å: Chain B: N.169, F.170, C.301, C.302 Ligands: NAD.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.302 2NO.13: 3 residues within 4Å: Chain C: N.169, C.302 Ligands: NAD.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:C.302 2NO.18: 5 residues within 4Å: Chain D: N.169, F.170, C.301, C.302 Ligands: NAD.19 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:C.302

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

NAD.2: 29 residues within 4Å: Chain A: 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, 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: 2NO.1, MG.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.167 Hydrogen bonds: A:I.166, A:N.169, A:E.195, A:Q.196, A:G.245, A:S.246, A:Q.349, A:K.352, A:K.352 Water bridges: A:E.195, A:G.225 pi-Stacking: A:F.401 NAD.9: 30 residues within 4Å: Chain B: 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: 2NO.8, MG.10 16 PLIP interactions: 16 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:Q.349, B:K.352, B:K.352, B:E.399 Water bridges: B:E.195, B:G.225 pi-Stacking: B:F.401 NAD.15: 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: 2NO.13, MG.14 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:P.167 Hydrogen bonds: C:I.166, C:N.169, C:E.195, C:Q.196, C:G.245, C:S.246, C:S.246, C:C.302, C:Q.349, C:K.352, C:K.352 Water bridges: C:W.168, C:E.195, C:E.195, C:G.225 pi-Stacking: C:F.401 NAD.19: 29 residues within 4Å: Chain D: 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, L.269, G.270, C.302, Q.349, K.352, E.399, F.401 Ligands: 2NO.18, MG.20 12 PLIP interactions: 12 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:S.246, D:S.246, D:L.269, D:Q.349 Water bridges: D:G.225 pi-Stacking: D:F.401

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

MG.3: 1 residues within 4Å: Ligands: NAD.2 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: NAD.9 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: NAD.15 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Ligands: NAD.19 No protein-ligand interaction detected (PLIP)

6 x URE: UREA(Non-functional Binders)

URE.4: 5 residues within 4Å: Chain A: F.70, E.157, P.158, V.159 Chain B: Q.447 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:Q.447, A:E.157, A:P.158, A:P.158 Water bridges: A:R.77, A:R.77, A:R.77, A:R.77 URE.6: 5 residues within 4Å: Chain A: F.151 Chain C: N.440, S.443 Chain D: Y.153, R.155 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.440, C:S.443, D:R.155 URE.7: 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 B, 2 interactions with chain A Hydrogen bonds: B:R.155, A:N.440, A:N.440 URE.11: 6 residues within 4Å: Chain A: Q.447, Y.468 Chain B: F.70, E.157, P.158, V.159 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.157, B:P.158, B:P.158, A:Q.447 Water bridges: B:R.77, B:R.77 URE.16: 6 residues within 4Å: Chain C: F.70, E.157, P.158, V.159 Chain D: Q.447, Y.468 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:P.158, C:P.158, D:Q.447 Water bridges: C:R.77, C:R.77 URE.21: 6 residues within 4Å: Chain C: Q.447, Y.468 Chain D: F.70, E.157, P.158, V.159 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:P.158, D:P.158, C:Q.447 Water bridges: D:R.77, D:R.77, D:R.77, D:R.77

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

NA.5: 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, A:Q.196 NA.12: 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, B:V.40 NA.17: 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 Water bridges: C:T.39 NA.22: 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 Water bridges: D:T.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lang, B.S. et al., Vascular Bioactivation of Nitroglycerin by Aldehyde Dehydrogenase-2: REACTION INTERMEDIATES REVEALED BY CRYSTALLOGRAPHY AND MASS SPECTROMETRY. J.Biol.Chem. (2012)

Release Date

2012-09-26

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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