SMTL ID : 8dr9.1

Crystal structure of human ALDH2 in complex with NAD+ and PEG MME 550

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 5 residues within 4Å: Chain A: H.30, D.31, V.33, R.35, K.62 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.31 Hydrogen bonds: A:D.31, A:D.31, A:R.35, A:R.35 Water bridges: A:K.62, A:K.62 Salt bridges: A:H.30, A:R.35, A:K.62, A:K.62 CIT.9: 9 residues within 4Å: Chain B: M.279, S.280, D.281, Q.312, K.412, T.413, I.414, E.415, K.439 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.280, B:S.280, B:D.281, B:I.414 Salt bridges: B:K.439, B:K.439 CIT.16: 5 residues within 4Å: Chain C: H.30, D.31, V.33, R.35, K.62 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:D.31 Hydrogen bonds: C:D.31, C:D.31, C:R.35, C:R.35 Water bridges: C:K.62, C:K.62 Salt bridges: C:H.30, C:R.35, C:K.62, C:K.62 CIT.24: 9 residues within 4Å: Chain D: M.279, S.280, D.281, Q.312, K.412, T.413, I.414, E.415, K.439 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.280, D:S.280, D:D.281, D:I.414 Salt bridges: D:K.439, D:K.439

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

NAD.2: 25 residues within 4Å: Chain A: I.166, I.167, P.168, W.169, K.193, A.195, E.196, F.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, E.249, I.250, V.253, I.254, T.349, Q.350, K.353, E.400, F.402 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:I.167, A:K.193, A:E.196, A:S.247, A:E.249, A:Q.350, A:K.353, A:E.400, A:E.400 Water bridges: A:W.169, A:W.169, A:W.169, A:G.226, A:S.247, A:S.247, A:T.248, A:V.253, A:K.353, A:E.400 NAD.10: 28 residues within 4Å: Chain B: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, I.250, V.253, I.254, E.269, L.270, G.271, S.303, E.400, F.402, L.428, F.466 Ligands: 1PE.12 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.168, B:T.245 Hydrogen bonds: B:I.167, B:K.193, B:E.196, B:S.247, B:E.269, B:S.303, B:E.400 Water bridges: B:W.169, B:W.169, B:Q.197, B:G.226, B:T.248, B:E.400, B:E.400 NAD.17: 25 residues within 4Å: Chain C: I.166, I.167, P.168, W.169, K.193, A.195, E.196, F.225, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, E.249, I.250, V.253, I.254, T.349, Q.350, K.353, E.400, F.402 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:I.167, C:K.193, C:E.196, C:S.247, C:E.249, C:Q.350, C:K.353, C:E.400 Water bridges: C:W.169, C:W.169, C:W.169, C:G.226, C:S.247, C:S.247, C:T.248, C:V.253, C:K.353, C:E.400 NAD.25: 28 residues within 4Å: Chain D: I.166, I.167, P.168, W.169, N.170, K.193, A.195, E.196, G.226, P.227, G.230, A.231, F.244, T.245, G.246, S.247, I.250, V.253, I.254, E.269, L.270, G.271, S.303, E.400, F.402, L.428, F.466 Ligands: 1PE.27 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:P.168, D:T.245 Hydrogen bonds: D:I.167, D:K.193, D:E.196, D:S.247, D:E.269, D:E.269, D:S.303, D:E.400 Water bridges: D:W.169, D:W.169, D:Q.197, D:G.226, D:T.248

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

NA.3: 4 residues within 4Å: Chain A: T.40, V.41, D.110, Q.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.41, A:D.110, A:D.110 NA.11: 4 residues within 4Å: Chain B: T.40, V.41, D.110, Q.197 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.40, B:V.41 Water bridges: B:T.40 NA.18: 4 residues within 4Å: Chain C: T.40, V.41, D.110, Q.197 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.41, C:D.110 Water bridges: C:T.40 NA.26: 4 residues within 4Å: Chain D: T.40, V.41, D.110, Q.197 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.41, D:V.41, D:D.110

18 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 3 residues within 4Å: Chain A: E.318, E.321, R.322 Ligand excluded by PLIP 1PE.5: 11 residues within 4Å: Chain A: V.121, M.125, F.171, L.174, M.175, F.293, F.297, C.302, D.458, F.460, F.466 Ligand excluded by PLIP 1PE.6: 4 residues within 4Å: Chain A: E.416, G.419, R.420, N.423 Ligand excluded by PLIP 1PE.7: 5 residues within 4Å: Chain A: E.313, Y.316, D.317, D.389, K.410 Ligand excluded by PLIP 1PE.8: 5 residues within 4Å: Chain A: D.283, W.286, N.455 Chain B: K.495 Chain D: D.438 Ligand excluded by PLIP 1PE.12: 12 residues within 4Å: Chain B: V.121, M.125, F.171, L.174, W.178, F.293, F.297, C.302, D.458, F.460, F.466 Ligands: NAD.10 Ligand excluded by PLIP 1PE.13: 3 residues within 4Å: Chain B: D.392, K.398, N.423 Ligand excluded by PLIP 1PE.14: 5 residues within 4Å: Chain B: V.332, G.333, N.334, A.375, A.376 Ligand excluded by PLIP 1PE.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP 1PE.19: 3 residues within 4Å: Chain C: E.318, E.321, R.322 Ligand excluded by PLIP 1PE.20: 11 residues within 4Å: Chain C: V.121, M.125, F.171, L.174, M.175, F.293, F.297, C.302, D.458, F.460, F.466 Ligand excluded by PLIP 1PE.21: 4 residues within 4Å: Chain C: E.416, G.419, R.420, N.423 Ligand excluded by PLIP 1PE.22: 5 residues within 4Å: Chain C: E.313, Y.316, D.317, D.389, K.410 Ligand excluded by PLIP 1PE.23: 5 residues within 4Å: Chain B: D.438 Chain C: D.283, W.286, N.455 Chain D: K.495 Ligand excluded by PLIP 1PE.27: 12 residues within 4Å: Chain D: V.121, M.125, F.171, L.174, W.178, F.293, F.297, C.302, D.458, F.460, F.466 Ligands: NAD.25 Ligand excluded by PLIP 1PE.28: 3 residues within 4Å: Chain D: D.392, K.398, N.423 Ligand excluded by PLIP 1PE.29: 5 residues within 4Å: Chain D: V.332, G.333, N.334, A.375, A.376 Ligand excluded by PLIP 1PE.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, S.Y. et al., Crystal structure of human ALDH2 in complex with NAD+ and PEG MME 550. To be published

Release Date

2023-08-30

Peptides

Aldehyde dehydrogenase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Aldehyde dehydrogenase, mitochondrial