SMTL ID : 6o4c.1 (1 other biounit)

Structure of ALDH7A1 mutant W175A complexed with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: I.165, T.166, A.167, F.168, N.169, K.192, G.193, A.194, P.195, A.229, G.232, T.233, F.246, T.247, G.248, S.249, V.252, V.256, E.270, L.271, G.272, G.273, C.304, E.401, F.403, L.429, F.470 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.247 Hydrogen bonds: A:T.166, A:F.168, A:K.192, A:T.233, A:T.233, A:S.249, A:E.270, A:L.271, A:G.273, A:E.401 Water bridges: A:A.229, A:S.249, A:S.249, A:T.250, A:R.308, A:E.401 NAD.6: 27 residues within 4Å: Chain B: I.165, T.166, A.167, F.168, N.169, K.192, G.193, A.194, P.195, A.229, G.232, T.233, F.246, T.247, G.248, S.249, V.252, V.256, E.270, L.271, G.272, G.273, C.304, E.401, F.403, F.470 Ligands: MG.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.247 Hydrogen bonds: B:T.166, B:F.168, B:K.192, B:T.233, B:S.249, B:L.271, B:G.273, B:E.401 Water bridges: B:A.229, B:S.249, B:S.249, B:T.250, B:R.308, B:E.401, B:E.401 NAD.10: 27 residues within 4Å: Chain C: I.165, T.166, A.167, F.168, N.169, K.192, G.193, A.194, P.195, A.229, G.232, T.233, F.246, T.247, G.248, S.249, V.252, V.256, E.270, L.271, G.272, G.273, C.304, E.401, F.403, L.429, F.470 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:T.247 Hydrogen bonds: C:T.166, C:F.168, C:K.192, C:T.233, C:T.233, C:S.249, C:L.271, C:G.273, C:E.401 Water bridges: C:A.229, C:T.250, C:R.308 NAD.15: 27 residues within 4Å: Chain D: I.165, T.166, A.167, F.168, N.169, K.192, G.193, A.194, P.195, A.229, G.232, T.233, F.246, T.247, G.248, S.249, V.252, V.256, E.270, L.271, G.272, G.273, C.304, E.401, F.403, L.429, F.470 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:T.247 Hydrogen bonds: D:T.166, D:F.168, D:K.192, D:T.233, D:S.249, D:E.270, D:L.271, D:G.273, D:E.401 Water bridges: D:A.229, D:T.250, D:R.308, D:E.401

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 5 residues within 4Å: Chain A: F.170, V.174, A.177, F.470, E.481 No protein-ligand interaction detected (PLIP) PGE.7: 6 residues within 4Å: Chain B: F.170, V.174, C.304, E.465, F.470, E.481 No protein-ligand interaction detected (PLIP) PGE.11: 7 residues within 4Å: Chain C: E.123, F.170, V.174, A.177, C.304, F.470, E.481 No protein-ligand interaction detected (PLIP) PGE.16: 8 residues within 4Å: Chain D: F.170, V.174, A.177, C.304, E.465, I.466, F.470, E.481 No protein-ligand interaction detected (PLIP)

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

1PE.3: 5 residues within 4Å: Chain A: R.70, W.73, V.159, G.160, N.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.70, A:R.70, A:N.242 1PE.8: 7 residues within 4Å: Chain B: R.70, E.71, W.73, V.159, G.160, E.239, N.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.70, B:R.70, B:N.242 1PE.12: 9 residues within 4Å: Chain C: R.70, E.71, W.73, K.74, V.159, G.160, E.239, R.240, N.242 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.70, C:R.70, C:N.242 1PE.17: 6 residues within 4Å: Chain D: R.70, E.71, W.73, V.159, E.239, N.242 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.70, D:R.70, D:E.239, D:N.242 Water bridges: D:R.70, D:E.71, D:E.71

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: F.512, Q.513 Chain B: V.289, R.323 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: V.289, R.323 Chain B: F.512, Q.513 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain C: F.512, Q.513 Chain D: V.289, R.323 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain C: V.289, R.323 Chain D: F.512, Q.513 Ligand excluded by PLIP

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

MG.9: 1 residues within 4Å: Ligands: NAD.6 No protein-ligand interaction detected (PLIP)

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

EDO.13: 3 residues within 4Å: Chain C: W.15, V.101, S.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.104 Water bridges: C:W.337 EDO.14: 6 residues within 4Å: Chain C: Y.328, A.329, I.331, V.333, Y.371, P.385 No protein-ligand interaction detected (PLIP) EDO.18: 3 residues within 4Å: Chain B: Y.500, S.501 Chain D: R.443 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.443, B:Y.500 Water bridges: B:G.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laciak, A.R. et al., Structural and biochemical consequences of pyridoxine-dependent epilepsy mutations that target the aldehyde binding site of aldehyde dehydrogenase ALDH7A1. Febs J. (2020)

Release Date

2019-07-24

Peptides

Alpha-aminoadipic semialdehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Alpha-aminoadipic semialdehyde dehydrogenase

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