SMTL ID : 8of3.1

Structure of the apoform of ALDEHYDE DEHYDROGENASE 5F1 (ALDH5F1) from the moss Physcomitrium patens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

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

P33.1: 25 residues within 4Å: Chain A: F.85, S.89, K.90, V.150, Y.151, G.152, V.166, M.167, K.168, Q.169, P.170, V.171, G.172, R.251, 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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.168, A:Q.169, A:V.171 Water bridges: C:K.480 P33.9: 25 residues within 4Å: Chain B: F.85, S.89, K.90, V.150, G.152, V.166, 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 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Water bridges: D:E.455, D:K.480 Hydrogen bonds: B:K.168, B:K.168, B:Q.169 P33.21: 25 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, V.150, Y.151, G.152, V.166, M.167, K.168, Q.169, P.170, V.171, G.172, R.251, E.498, K.500 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Water bridges: A:E.458, A:E.458, A:K.480 Hydrogen bonds: C:K.168, C:Q.169, C:V.171 P33.29: 25 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, V.150, G.152, V.166, M.167, K.168, Q.169, P.170, V.171, G.172, R.251, E.498, K.500 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:K.168, D:K.168, D:Q.169 Water bridges: B:E.458, B:E.458, B:K.480

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

PGE.2: 8 residues within 4Å: Chain A: P.158, F.159, P.160, E.161 Chain C: V.134, Y.135, A.138 Chain D: N.94 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Water bridges: A:E.161, A:E.161, D:N.94 PGE.10: 7 residues within 4Å: Chain B: P.158, F.159, P.160 Chain C: N.94 Chain D: V.134, Y.135, A.138 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.134 Water bridges: D:E.472 PGE.11: 8 residues within 4Å: Chain B: A.127, E.128, G.131, E.132, Y.135, F.182, R.307, S.470 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.307 Water bridges: B:E.128, B:E.128, B:Y.135 PGE.22: 8 residues within 4Å: Chain A: V.134, Y.135, A.138 Chain B: N.94 Chain C: P.158, F.159, P.160, E.161 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:E.161, C:E.161, B:N.94 PGE.30: 7 residues within 4Å: Chain A: N.94 Chain B: V.134, Y.135, A.138 Chain D: P.158, F.159, P.160 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.134 Water bridges: B:E.472 PGE.31: 8 residues within 4Å: Chain D: A.127, E.128, G.131, E.132, Y.135, F.182, R.307, S.470 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.307 Water bridges: D:E.128, D:Y.135

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

1PE.3: 11 residues within 4Å: Chain A: A.127, E.128, G.131, E.132, Y.135, F.182, R.307, T.312, V.314, L.468, S.470 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.307, A:R.307 Water bridges: A:S.470, A:S.470, A:S.470 1PE.23: 11 residues within 4Å: Chain C: A.127, E.128, G.131, E.132, Y.135, F.182, R.307, T.312, V.314, L.468, S.470 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.307, C:R.307 Water bridges: C:S.470, C:S.470, C:S.470

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

EDO.4: 8 residues within 4Å: Chain A: E.128, L.302, A.303, Y.306, R.307, L.340, T.351, Q.352 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: I.78, D.246, S.247, T.248, E.249 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: I.177, K.204, A.237, K.238, G.241, F.255, V.261 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain B: P.179, W.180, N.181, M.186, T.256, G.257, S.258, C.313, F.412 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: R.17, G.18, G.60, E.61, I.62 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain B: L.302, A.303, Y.306, R.307, L.340, T.351, Q.352 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: I.177, K.204, A.237, G.241, F.255, G.257, V.261 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: L.38, G.40, D.41, K.42, W.43, L.221, P.227 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: I.78, D.246, S.247, T.248, E.249 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain C: E.128, L.302, A.303, Y.306, R.307, L.340, T.351, Q.352 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain C: I.78, D.246, S.247, T.248, E.249 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain C: I.177, K.204, A.237, K.238, G.241, F.255, V.261 Ligand excluded by PLIP EDO.32: 9 residues within 4Å: Chain D: P.179, W.180, N.181, M.186, T.256, G.257, S.258, C.313, F.412 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain D: R.17, G.18, G.60, E.61, I.62 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain D: L.302, A.303, Y.306, R.307, L.340, T.351, Q.352 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain D: I.177, K.204, A.237, G.241, F.255, G.257, V.261 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain D: L.38, G.40, D.41, K.42, W.43, L.221, P.227 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain D: I.78, D.246, S.247, T.248, E.249 Ligand excluded by PLIP

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

SO4.5: 4 residues within 4Å: Chain A: L.340, R.341, A.342, H.385 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.341, A:A.342 Water bridges: A:H.385 Salt bridges: A:H.385 SO4.6: 3 residues within 4Å: Chain A: N.357, E.358, T.359 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.357, A:E.358, A:T.359, A:T.359 SO4.16: 4 residues within 4Å: Chain B: L.340, R.341, A.342, H.385 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.340, B:A.342 Water bridges: B:R.341, B:H.385, B:H.385 Salt bridges: B:R.341, B:H.385 SO4.17: 3 residues within 4Å: Chain B: N.357, E.358, T.359 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.357, B:N.357, B:E.358, B:T.359, B:T.359 SO4.18: 4 residues within 4Å: Chain B: H.20, M.21, G.22, T.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.20, B:H.20, B:G.22, B:T.23 SO4.25: 4 residues within 4Å: Chain C: L.340, R.341, A.342, H.385 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.341, C:A.342 Water bridges: C:H.385 Salt bridges: C:H.385 SO4.26: 3 residues within 4Å: Chain C: N.357, E.358, T.359 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.357, C:E.358, C:T.359, C:T.359 SO4.36: 4 residues within 4Å: Chain D: L.340, R.341, A.342, H.385 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:L.340, D:A.342 Water bridges: D:R.341, D:H.385, D:H.385 Salt bridges: D:R.341, D:H.385 SO4.37: 3 residues within 4Å: Chain D: N.357, E.358, T.359 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.357, D:N.357, D:E.358, D:T.359, D:T.359 SO4.38: 4 residues within 4Å: Chain D: H.20, M.21, G.22, T.23 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.20, D:H.20, D:G.22, D:T.23

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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