SMTL ID : 6o4c.2 (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, F.470 Ligands: MG.7 15 PLIP interactions: 15 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:T.250, A:R.308, A:E.401 NAD.8: 28 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, L.429, F.470 Ligands: MG.12 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.13: 26 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, F.470 16 PLIP interactions: 16 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:S.249, C:T.250, C:R.308, C:E.401, C:E.401 NAD.20: 26 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, F.470 15 PLIP interactions: 15 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:S.249, D:S.249, D:T.250, D:E.401

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

PGE.2: 4 residues within 4Å: Chain A: F.170, E.465, F.470, E.481 No protein-ligand interaction detected (PLIP) PGE.9: 8 residues within 4Å: Chain B: F.170, V.174, C.304, E.465, I.466, F.470, E.481, S.482 No protein-ligand interaction detected (PLIP) PGE.14: 6 residues within 4Å: Chain C: F.170, A.177, C.304, E.465, F.470, E.481 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.465 PGE.22: 5 residues within 4Å: Chain D: Y.328, I.331, V.333, Y.371, P.385 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.371

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: Y.328, I.331, V.333, Y.371, P.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.371

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

1PE.4: 8 residues within 4Å: Chain A: R.70, E.71, W.73, V.159, G.160, E.239, R.240, N.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.70, A:R.70, A:N.242 Water bridges: A:E.71 1PE.10: 7 residues within 4Å: Chain B: R.70, W.73, V.159, G.160, E.239, R.240, N.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.70, B:R.70, B:N.242 1PE.15: 8 residues within 4Å: Chain C: R.70, E.71, W.73, 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.23: 8 residues within 4Å: Chain D: R.70, W.73, K.74, V.159, G.160, E.239, R.240, N.242 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.70, D:R.70, D:N.242

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

CL.5: 4 residues within 4Å: Chain A: F.512, Q.513 Chain B: V.289, R.323 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: V.289, R.323 Chain B: F.512, Q.513 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: F.512, Q.513 Chain D: V.289, R.323 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain C: V.289, R.323 Chain D: F.512, Q.513 Ligand excluded by PLIP

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

MG.7: 1 residues within 4Å: Ligands: NAD.1 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: NAD.8 No protein-ligand interaction detected (PLIP)

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

EDO.11: 4 residues within 4Å: Chain B: Y.130, L.134, S.484 Chain D: M.137 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.130, B:S.484 Water bridges: D:M.137 EDO.16: 4 residues within 4Å: Chain C: W.15, Q.100, V.101, S.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.100, C:S.104 EDO.17: 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.24: 3 residues within 4Å: Chain D: W.15, V.101, S.104 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.104 Water bridges: D:S.104

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.21: 10 residues within 4Å: Chain D: E.123, F.170, V.174, A.177, C.304, T.305, S.462, E.465, F.470, E.481 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.305, D:S.462, D:E.465 Water bridges: D:E.465

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
E

B
F

C
G

D
H

Alpha-aminoadipic semialdehyde dehydrogenase

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