SMTL ID : 4fr8.1 (1 other biounit)

Crystal structure of human aldehyde dehydrogenase-2 in complex with nitroglycerin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

1 x TNG: propane-1,2,3-triyl trinitrate(Non-covalent)

TNG.1: 13 residues within 4Å: Chain A: N.169, F.170, L.173, M.174, W.177, Q.268, F.296, S.301, C.302, S.303, D.457, F.459, F.465 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.457

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

NAD.2: 23 residues within 4Å: Chain A: I.165, I.166, W.168, 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, V.252, I.253, Q.349, K.352, E.399, F.401 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:I.166, A:K.192, A:E.195, A:Q.196, A:S.246, A:Q.349, A:K.352, A:E.399 Water bridges: A:E.195, A:E.195, A:Q.196, A:S.246, A:S.246, A:E.399, A:I.400 NAD.10: 23 residues within 4Å: Chain C: I.165, I.166, W.168, 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, V.252, I.253, Q.349, K.352, E.399, F.401 Ligands: MG.11 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:I.166, C:K.192, C:E.195, C:Q.196, C:S.246, C:Q.349, C:Q.349, C:K.352 Water bridges: C:E.195, C:E.195, C:S.246 NAD.15: 23 residues within 4Å: Chain D: I.165, I.166, W.168, 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, V.252, I.253, Q.349, K.352, E.399, F.401 Ligands: MG.16 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:I.166, D:K.192, D:E.195, D:Q.196, D:S.246, D:S.246, D:Q.349, D:Q.349, D:K.352 Water bridges: D:W.168, D:Q.196, D:G.225, D:E.399, D:I.400

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

MG.3: 1 residues within 4Å: Ligands: NAD.2 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: NAD.10 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: NAD.15 No protein-ligand interaction detected (PLIP)

5 x URE: UREA(Non-functional Binders)

URE.4: 6 residues within 4Å: Chain A: F.70, E.157, P.158, V.159 Chain B: Q.447, Y.468 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.157, A:P.158, A:P.158 Water bridges: A:R.77 URE.8: 6 residues within 4Å: Chain A: Q.447, Y.468 Chain B: F.70, E.157, P.158, V.159 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.468, B:E.157, B:E.157, B:P.158 Water bridges: A:Q.447 URE.12: 6 residues within 4Å: Chain C: F.70, E.157, P.158, V.159 Chain D: Q.447, Y.468 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:P.158, C:P.158 Water bridges: C:R.77 URE.14: 4 residues within 4Å: Chain C: Q.13, N.333, F.335, D.336 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.13, C:Q.13, C:D.336 URE.17: 5 residues within 4Å: Chain C: Y.468 Chain D: F.70, E.157, P.158, V.159 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.158, D:P.158 Water bridges: 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 Water bridges: A:T.39 NA.9: 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:D.109 NA.13: 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:V.40, C:D.109 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 Water bridges: D:T.39

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 19 residues within 4Å: Chain B: I.165, I.166, W.168, 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, V.252, I.253 Ligands: MG.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:I.166, B:K.192, B:E.195, B:Q.196, B:S.246, B:S.246, B:S.246 Water bridges: B:G.225

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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