SMTL ID : 8ofm.1

Structure of the ALDEHYDE DEHYDROGENASE 5F1 (ALDH5F1) from the moss Physcomitrium patens in complex with NAD in an extended conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: E.128, L.302, A.303, Y.306, R.307, L.340, T.351, Q.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.128 Water bridges: A:A.303 EDO.14: 7 residues within 4Å: Chain A: W.180, L.208, I.356, N.357, T.359, A.360 Ligands: NAD.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.357 EDO.15: 7 residues within 4Å: Chain A: D.291, E.445, N.446 Chain D: D.291, E.445, N.446, I.447 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.446, D:N.446 Water bridges: A:D.291 EDO.16: 3 residues within 4Å: Chain A: R.384, G.388, R.389 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.384, A:R.384, A:R.389 EDO.17: 4 residues within 4Å: Chain A: R.101, N.105 Chain B: R.101, N.105 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.105, B:N.105 Water bridges: A:R.101, A:N.105, B:R.101, B:R.101 EDO.36: 8 residues within 4Å: Chain C: E.128, L.302, A.303, Y.306, R.307, L.340, T.351, Q.352 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.128, C:E.128 Water bridges: C:A.303 EDO.49: 7 residues within 4Å: Chain C: W.180, L.208, I.356, N.357, T.359, A.360 Ligands: NAD.41 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.357 EDO.50: 7 residues within 4Å: Chain B: D.291, E.445, N.446, I.447 Chain C: D.291, E.445, N.446 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.446, C:N.446 Water bridges: B:D.291 EDO.51: 3 residues within 4Å: Chain C: R.384, G.388, R.389 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.384, C:R.384, C:R.389 EDO.52: 4 residues within 4Å: Chain C: R.101, N.105 Chain D: R.101, N.105 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:N.105, C:N.105 Water bridges: D:R.101, D:R.101, C:R.101, C:N.105

26 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: L.38, G.40, D.41, K.42, W.43, L.221, P.227 Ligands: GOL.19 Ligand excluded by PLIP GOL.3: 11 residues within 4Å: Chain A: V.150, Y.151, G.152, M.167, K.168, Q.169 Chain D: I.154, I.155, P.156, S.157, R.163 Ligand excluded by PLIP GOL.4: 11 residues within 4Å: Chain A: F.85, Q.169, P.170, V.171, G.172, R.251, E.498 Chain C: E.458, M.479, K.480 Ligands: GOL.5 Ligand excluded by PLIP GOL.5: 11 residues within 4Å: Chain A: S.82, F.85, V.171, G.172, V.173, E.249, V.250, R.251 Chain C: E.458, K.480 Ligands: GOL.4 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain A: K.299, G.300, A.303, F.443, E.466, G.467, L.468 Chain C: K.162 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain A: K.34, W.43, E.218, L.221 Ligands: GOL.2 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain B: L.38, G.40, D.41, K.42, W.43, L.221, P.227 Ligands: GOL.22 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: K.34, W.43, E.218, L.221, Q.222 Ligands: GOL.21 Ligand excluded by PLIP GOL.23: 12 residues within 4Å: Chain B: V.150, Y.151, G.152, M.167, K.168, Q.169 Chain C: I.154, I.155, P.156, S.157, R.163 Chain D: W.451 Ligand excluded by PLIP GOL.24: 9 residues within 4Å: Chain B: F.85, V.171, G.172, V.173, E.249, R.251 Chain D: E.458, K.480 Ligands: GOL.25 Ligand excluded by PLIP GOL.25: 11 residues within 4Å: Chain B: F.85, Q.169, P.170, V.171, G.172, R.251, E.498 Chain D: E.458, M.479, K.480 Ligands: GOL.24 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain B: K.299, G.300, A.303, E.466, G.467, L.468 Chain D: K.162 Ligand excluded by PLIP GOL.35: 9 residues within 4Å: Chain B: E.128, L.302, A.303, Y.306, R.307, N.308, L.340, T.351, Q.352 Ligand excluded by PLIP GOL.37: 8 residues within 4Å: Chain C: L.38, G.40, D.41, K.42, W.43, L.221, P.227 Ligands: GOL.54 Ligand excluded by PLIP GOL.38: 11 residues within 4Å: Chain B: I.154, I.155, P.156, S.157, R.163 Chain C: V.150, Y.151, G.152, M.167, K.168, Q.169 Ligand excluded by PLIP GOL.39: 11 residues within 4Å: Chain A: E.458, M.479, K.480 Chain C: F.85, Q.169, P.170, V.171, G.172, R.251, E.498 Ligands: GOL.40 Ligand excluded by PLIP GOL.40: 11 residues within 4Å: Chain A: E.458, K.480 Chain C: S.82, F.85, V.171, G.172, V.173, E.249, V.250, R.251 Ligands: GOL.39 Ligand excluded by PLIP GOL.53: 8 residues within 4Å: Chain A: K.162 Chain C: K.299, G.300, A.303, F.443, E.466, G.467, L.468 Ligand excluded by PLIP GOL.54: 5 residues within 4Å: Chain C: K.34, W.43, E.218, L.221 Ligands: GOL.37 Ligand excluded by PLIP GOL.56: 8 residues within 4Å: Chain D: L.38, G.40, D.41, K.42, W.43, L.221, P.227 Ligands: GOL.57 Ligand excluded by PLIP GOL.57: 6 residues within 4Å: Chain D: K.34, W.43, E.218, L.221, Q.222 Ligands: GOL.56 Ligand excluded by PLIP GOL.58: 12 residues within 4Å: Chain A: I.154, I.155, P.156, S.157, R.163 Chain B: W.451 Chain D: V.150, Y.151, G.152, M.167, K.168, Q.169 Ligand excluded by PLIP GOL.59: 9 residues within 4Å: Chain B: E.458, K.480 Chain D: F.85, V.171, G.172, V.173, E.249, R.251 Ligands: GOL.60 Ligand excluded by PLIP GOL.60: 11 residues within 4Å: Chain B: E.458, M.479, K.480 Chain D: F.85, Q.169, P.170, V.171, G.172, R.251, E.498 Ligands: GOL.59 Ligand excluded by PLIP GOL.69: 7 residues within 4Å: Chain B: K.162 Chain D: K.299, G.300, A.303, E.466, G.467, L.468 Ligand excluded by PLIP GOL.70: 9 residues within 4Å: Chain D: E.128, L.302, A.303, Y.306, R.307, N.308, L.340, T.351, Q.352 Ligand excluded by PLIP

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

NAD.6: 33 residues within 4Å: Chain A: I.177, A.178, P.179, W.180, N.181, F.182, 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, T.312, C.313, V.314, K.363, E.410, F.412, L.438 Ligands: SO4.11, EDO.14 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.256, A:E.279 Hydrogen bonds: A:A.178, A:W.180, A:W.180, A:N.181, A:K.204, A:S.258, A:S.258, A:E.279, A:C.313, A:E.410, A:E.410 Water bridges: A:K.238, A:G.281 NAD.20: 31 residues within 4Å: Chain B: I.177, A.178, P.179, W.180, N.181, F.182, 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, L.265, E.279, L.280, G.281, T.312, C.313, V.314, K.363, E.410, F.412, L.438 Ligands: SO4.32 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.256, B:E.279 Hydrogen bonds: B:A.178, B:W.180, B:W.180, B:N.181, B:K.204, B:S.258, B:S.258, B:E.279, B:C.313, B:E.410, B:E.410 Water bridges: B:S.206, B:E.207, B:E.207, B:E.207, B:K.238, B:T.259 NAD.41: 33 residues within 4Å: Chain C: I.177, A.178, P.179, W.180, N.181, F.182, 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, T.312, C.313, V.314, K.363, E.410, F.412, L.438 Ligands: SO4.46, EDO.49 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:T.256, C:E.279 Hydrogen bonds: C:A.178, C:W.180, C:W.180, C:N.181, C:K.204, C:S.258, C:S.258, C:E.279, C:E.279, C:C.313, C:E.410, C:E.410 Water bridges: C:K.238, C:G.281 NAD.55: 31 residues within 4Å: Chain D: I.177, A.178, P.179, W.180, N.181, F.182, 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, L.265, E.279, L.280, G.281, T.312, C.313, V.314, K.363, E.410, F.412, L.438 Ligands: SO4.67 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:T.256, D:E.279 Hydrogen bonds: D:A.178, D:W.180, D:W.180, D:N.181, D:K.204, D:S.258, D:S.258, D:E.279, D:E.279, D:C.313, D:E.410, D:E.410 Water bridges: D:S.206, D:E.207, D:K.238, D:T.259

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

SO4.7: 4 residues within 4Å: Chain A: L.340, R.341, A.342, H.385 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: H.10, R.17 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: N.357, E.358, T.359 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: S.258, T.259, G.260 Ligand excluded by PLIP SO4.11: 10 residues within 4Å: Chain A: Y.135, F.182, M.186, R.189, T.312, C.313, V.314, S.470, F.476 Ligands: NAD.6 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: I.78, S.247, T.248, E.249 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain A: P.510, V.511, G.512 Chain B: K.429 Chain D: K.90 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain B: L.340, R.341, A.342, H.385 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain B: S.258, T.259, G.260, V.261 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain B: H.20, M.21, G.22, T.23 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain B: Q.36, K.42, W.43, V.44, D.45 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain B: R.17, G.60, E.61, I.62 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain B: N.357, E.358, T.359 Ligand excluded by PLIP SO4.32: 10 residues within 4Å: Chain B: Y.135, F.182, M.186, R.189, T.312, C.313, V.314, S.470, F.476 Ligands: NAD.20 Ligand excluded by PLIP SO4.33: 6 residues within 4Å: Chain B: G.131, E.132, Y.135, F.182, R.307, S.470 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain C: L.340, R.341, A.342, H.385 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain C: H.10, R.17 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain C: N.357, E.358, T.359 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain C: S.258, T.259, G.260 Ligand excluded by PLIP SO4.46: 10 residues within 4Å: Chain C: Y.135, F.182, M.186, R.189, T.312, C.313, V.314, S.470, F.476 Ligands: NAD.41 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain C: I.78, S.247, T.248, E.249 Ligand excluded by PLIP SO4.48: 5 residues within 4Å: Chain B: K.90 Chain C: P.510, V.511, G.512 Chain D: K.429 Ligand excluded by PLIP SO4.61: 4 residues within 4Å: Chain D: L.340, R.341, A.342, H.385 Ligand excluded by PLIP SO4.62: 4 residues within 4Å: Chain D: S.258, T.259, G.260, V.261 Ligand excluded by PLIP SO4.63: 4 residues within 4Å: Chain D: H.20, M.21, G.22, T.23 Ligand excluded by PLIP SO4.64: 5 residues within 4Å: Chain D: Q.36, K.42, W.43, V.44, D.45 Ligand excluded by PLIP SO4.65: 4 residues within 4Å: Chain D: R.17, G.60, E.61, I.62 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain D: N.357, E.358, T.359 Ligand excluded by PLIP SO4.67: 10 residues within 4Å: Chain D: Y.135, F.182, M.186, R.189, T.312, C.313, V.314, S.470, F.476 Ligands: NAD.55 Ligand excluded by PLIP SO4.68: 6 residues within 4Å: Chain D: G.131, E.132, Y.135, F.182, R.307, S.470 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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