SMTL ID : 8of1.1

Structure of ALDH5F1 from moss Physcomitrium patens in complex with NAD+ in the contracted conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: I.177, A.178, P.179, W.180, N.181, M.186, K.204, P.205, S.206, E.207, A.237, K.238, G.241, F.255, T.256, G.257, S.258, V.261, M.264, L.265, E.279, L.280, G.281, C.313, K.363, E.410, F.412, L.438 Ligands: EDO.6, EDO.7 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.179, A:F.412 Hydrogen bonds: A:A.178, A:W.180, A:N.181, A:K.204, A:G.257, A:G.257, A:S.258, A:S.258, A:K.363, A:E.410, A:E.410 Water bridges: A:S.206, A:A.237, A:K.238, A:T.259 NAD.15: 30 residues within 4Å: Chain B: I.177, A.178, P.179, W.180, N.181, M.186, K.204, P.205, S.206, E.207, A.237, K.238, G.241, F.255, T.256, G.257, S.258, V.261, M.264, L.265, E.279, L.280, G.281, C.313, K.363, E.410, F.412, L.438 Ligands: PEG.17, EDO.20 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:P.179, B:F.412 Hydrogen bonds: B:A.178, B:W.180, B:N.181, B:K.204, B:E.207, B:G.257, B:G.257, B:S.258, B:S.258, B:C.313, B:K.363, B:E.410 Water bridges: B:E.207, B:E.207, B:A.237, B:K.238, B:T.259 NAD.29: 30 residues within 4Å: Chain C: I.177, A.178, P.179, W.180, N.181, M.186, K.204, P.205, S.206, E.207, A.237, K.238, G.241, F.255, T.256, G.257, S.258, V.261, M.264, L.265, E.279, L.280, G.281, C.313, K.363, E.410, F.412, L.438 Ligands: EDO.34, EDO.35 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:P.179, C:F.412 Hydrogen bonds: C:A.178, C:W.180, C:N.181, C:K.204, C:G.257, C:G.257, C:S.258, C:S.258, C:K.363, C:E.410 Water bridges: C:S.206, C:A.237, C:K.238, C:T.259 NAD.43: 30 residues within 4Å: Chain D: I.177, A.178, P.179, W.180, N.181, M.186, K.204, P.205, S.206, E.207, A.237, K.238, G.241, F.255, T.256, G.257, S.258, V.261, M.264, L.265, E.279, L.280, G.281, C.313, K.363, E.410, F.412, L.438 Ligands: PEG.45, EDO.48 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:P.179, D:F.412 Hydrogen bonds: D:A.178, D:W.180, D:N.181, D:K.204, D:E.207, D:G.257, D:G.257, D:S.258, D:S.258, D:C.313, D:K.363, D:E.410, D:E.410 Water bridges: D:E.207, D:A.237, D:K.238, D:T.259

4 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.2: 22 residues within 4Å: Chain A: F.85, S.89, K.90, M.167, K.168, Q.169, P.170, V.171, G.172, R.251, K.275, E.498, K.500 Chain C: E.455, S.456, L.457, E.458, M.479, K.480 Chain D: I.154, R.163, P.510 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.169, A:E.498, C:K.480 Water bridges: A:K.168, A:R.251 P33.16: 22 residues within 4Å: Chain A: I.154, R.163, P.510 Chain B: W.451, E.455, S.456, L.457, E.458, M.479, K.480 Chain D: F.85, S.89, K.90, M.167, K.168, Q.169, P.170, V.171, G.172, R.251, E.498, K.500 10 PLIP interactions: 6 interactions with chain B, 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: B:W.451, B:E.455, D:Q.169, A:R.163 Water bridges: B:E.458, B:E.458, B:E.458, B:K.480, D:K.168, D:E.498 P33.30: 22 residues within 4Å: Chain A: E.455, S.456, L.457, E.458, M.479, K.480 Chain B: I.154, R.163, P.510 Chain C: F.85, S.89, K.90, M.167, K.168, Q.169, P.170, V.171, G.172, R.251, K.275, E.498, K.500 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.169, C:E.498, C:E.498, A:K.480 Water bridges: C:K.168, C:R.251 P33.44: 22 residues within 4Å: Chain B: F.85, S.89, K.90, M.167, K.168, Q.169, P.170, V.171, G.172, R.251, E.498, K.500 Chain C: I.154, R.163, P.510 Chain D: W.451, E.455, S.456, L.457, E.458, M.479, K.480 8 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B, 4 interactions with chain D Hydrogen bonds: C:R.163, B:Q.169, D:W.451, D:E.455, D:E.455 Water bridges: B:K.168, B:E.498, D:K.480

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

PEG.3: 11 residues within 4Å: Chain A: P.125, E.128, L.302, A.303, Y.306, R.307, N.308, S.309, L.340, T.351, Q.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.128 PEG.17: 8 residues within 4Å: Chain B: W.180, L.208, I.356, N.357, T.359, A.360 Ligands: NAD.15, SO4.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.357, B:N.357, B:A.360 PEG.18: 6 residues within 4Å: Chain B: L.38, D.41, K.42, W.43, L.221, P.227 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.43, B:L.221 PEG.31: 11 residues within 4Å: Chain C: P.125, E.128, L.302, A.303, Y.306, R.307, N.308, S.309, L.340, T.351, Q.352 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.128, C:E.128 PEG.45: 8 residues within 4Å: Chain D: W.180, L.208, I.356, N.357, T.359, A.360 Ligands: NAD.43, SO4.53 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.357, D:N.357, D:A.360 PEG.46: 6 residues within 4Å: Chain D: L.38, D.41, K.42, W.43, L.221, P.227 2 PLIP interactions: 2 interactions with chain D Water bridges: D:W.43, D:L.221

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

EDO.4: 4 residues within 4Å: Chain A: N.94 Chain D: P.158, F.159, P.160 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: I.78, D.246, S.247, T.248, E.249 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: S.258, T.259, G.260 Ligands: NAD.1 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: W.180, L.208, I.356, N.357, T.359, A.360 Ligands: NAD.1 Ligand excluded by PLIP EDO.8: 1 residues within 4Å: Chain A: K.42 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: T.86, K.90 Chain C: K.429 Chain D: P.510, V.511, G.512 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: E.132, Y.135, F.182, R.307, S.470 Chain C: F.159 Ligands: SO4.12 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain B: E.128, L.302, A.303, Y.306, R.307, L.340, T.351, Q.352 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: S.258, T.259, G.260, K.363 Ligands: NAD.15 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: I.78, D.246, S.247, T.248, E.249 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: G.131, E.132, Y.135, F.182, R.307, S.470 Chain D: F.159 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: P.158, F.159, P.160 Chain C: N.94 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain C: I.78, D.246, S.247, T.248, E.249 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: S.258, T.259, G.260 Ligands: NAD.29 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain C: W.180, L.208, I.356, N.357, T.359, A.360 Ligands: NAD.29 Ligand excluded by PLIP EDO.36: 1 residues within 4Å: Chain C: K.42 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain A: K.429 Chain B: P.510, V.511, G.512 Chain C: T.86, K.90 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain A: F.159 Chain C: E.132, Y.135, F.182, R.307, S.470 Ligands: SO4.40 Ligand excluded by PLIP EDO.47: 8 residues within 4Å: Chain D: E.128, L.302, A.303, Y.306, R.307, L.340, T.351, Q.352 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain D: S.258, T.259, G.260, K.363 Ligands: NAD.43 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain D: I.78, D.246, S.247, T.248, E.249 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain B: F.159 Chain D: G.131, E.132, Y.135, F.182, R.307, S.470 Ligand excluded by PLIP

20 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 4 residues within 4Å: Chain A: L.340, R.341, A.342, H.385 Ligand excluded by PLIP SO4.12: 11 residues within 4Å: Chain A: Y.135, F.182, M.186, R.189, R.307, T.312, C.313, V.314, S.470, F.476 Ligands: EDO.10 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: N.357, E.358, T.359 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: H.20, M.21, G.22, T.23 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: L.340, R.341, A.342, H.385 Ligand excluded by PLIP SO4.24: 11 residues within 4Å: Chain B: Y.135, F.182, M.186, R.189, E.279, R.307, T.312, C.313, V.314, S.470, F.476 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain B: N.357, E.358, T.359 Ligands: PEG.17 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: G.60, R.389 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain B: S.19, H.20, M.21, G.22, T.23 Ligand excluded by PLIP SO4.28: 1 residues within 4Å: Chain B: R.341 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain C: L.340, R.341, A.342, H.385 Ligand excluded by PLIP SO4.40: 11 residues within 4Å: Chain C: Y.135, F.182, M.186, R.189, R.307, T.312, C.313, V.314, S.470, F.476 Ligands: EDO.38 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain C: N.357, E.358, T.359 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain C: H.20, M.21, G.22, T.23 Ligand excluded by PLIP SO4.51: 4 residues within 4Å: Chain D: L.340, R.341, A.342, H.385 Ligand excluded by PLIP SO4.52: 11 residues within 4Å: Chain D: Y.135, F.182, M.186, R.189, E.279, R.307, T.312, C.313, V.314, S.470, F.476 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain D: N.357, E.358, T.359 Ligands: PEG.45 Ligand excluded by PLIP SO4.54: 2 residues within 4Å: Chain D: G.60, R.389 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain D: S.19, H.20, M.21, G.22, T.23 Ligand excluded by PLIP SO4.56: 1 residues within 4Å: Chain D: R.341 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kopecny, D.J. et al., A study on abiotic stress responses of aldehyde dehydrogenase (ALDH) superfamilies in moss and barley focused on members linked to the GABA shunt pathway. To Be Published

Release Date

2024-03-27

Peptides

Succinate-semialdehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Succinate-semialdehyde dehydrogenase

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