SMTL ID : 6uxj.1

Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP-glycine and 5-formyltetrahydrofolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)

PLG.1: 21 residues within 4Å: Chain A: S.41, S.107, G.108, S.109, N.112, H.136, G.191, S.192, D.217, A.219, H.220, T.243, H.245, K.246, R.391 Chain B: Y.61, Y.71, Y.106, G.291, G.292 Ligands: FFO.2 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:H.136, A:A.219 Hydrogen bonds: A:S.41, A:G.108, A:S.109, A:S.109, A:N.112, A:S.192, A:S.192, A:H.220, B:Y.61, B:E.63, B:Y.71, B:G.291, B:G.292 Water bridges: A:S.107, A:T.241, A:R.252 Salt bridges: A:H.220, A:H.245, A:K.246, A:R.391 pi-Stacking: A:H.136 PLG.7: 21 residues within 4Å: Chain A: Y.61, Y.71, Y.106, G.291, G.292 Chain B: S.41, S.107, G.108, S.109, N.112, H.136, G.191, S.192, D.217, A.219, H.220, T.243, H.245, K.246, R.391 Ligands: FFO.8 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:H.136, B:A.219 Hydrogen bonds: B:S.41, B:G.108, B:S.109, B:N.112, B:S.192, B:H.220, A:Y.61, A:G.291, A:G.292 Water bridges: B:S.107, B:T.241, B:R.252 Salt bridges: B:H.220, B:H.245, B:K.246, B:R.391 pi-Stacking: B:H.136 PLG.13: 21 residues within 4Å: Chain C: S.41, S.107, G.108, S.109, N.112, H.136, G.191, S.192, D.217, A.219, H.220, T.243, H.245, K.246, R.391 Chain D: Y.61, Y.71, Y.106, G.291, G.292 Ligands: FFO.14 23 PLIP interactions: 8 interactions with chain D, 15 interactions with chain C Hydrogen bonds: D:Y.61, D:E.63, D:E.63, D:Y.71, D:Y.71, D:Y.106, D:G.291, D:G.292, C:S.41, C:G.108, C:S.109, C:N.112, C:S.192, C:H.220 Hydrophobic interactions: C:H.136, C:A.219 Water bridges: C:S.107, C:R.252 Salt bridges: C:H.220, C:H.245, C:K.246, C:R.391 pi-Stacking: C:H.136 PLG.22: 21 residues within 4Å: Chain C: Y.61, Y.71, Y.106, G.291, G.292 Chain D: S.41, S.107, G.108, S.109, N.112, H.136, G.191, S.192, D.217, A.219, H.220, T.243, H.245, K.246, R.391 Ligands: FFO.23 23 PLIP interactions: 16 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:H.136, D:A.219 Hydrogen bonds: D:S.41, D:G.108, D:S.109, D:N.112, D:S.192, D:H.220, D:K.246, C:Y.61, C:Y.61, C:E.63, C:Y.71, C:Y.106, C:G.291, C:G.292 Water bridges: D:S.107, D:R.252 Salt bridges: D:H.220, D:H.245, D:K.246, D:R.391 pi-Stacking: D:H.136

4 x FFO: N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid(Non-covalent)

FFO.2: 20 residues within 4Å: Chain A: L.131, G.134, G.135, H.136, L.137, Y.141, S.192, A.193, N.374, N.376, A.384, R.391 Chain B: E.63, Y.70, Y.71, F.283, F.286, P.287 Ligands: PLG.1, EDO.3 25 PLIP interactions: 19 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.137, A:Y.141, A:A.384, A:A.384, B:F.286 Hydrogen bonds: A:G.134, A:G.135, A:G.135, A:L.137, A:Y.141, A:S.192, A:N.374, A:N.376, A:N.376, A:L.385, B:E.63, B:Y.70, B:Y.70, B:Y.70 Water bridges: A:K.147, A:K.147, A:K.147, A:A.384 Salt bridges: A:K.147 pi-Stacking: B:Y.70 FFO.8: 20 residues within 4Å: Chain A: E.63, Y.70, Y.71, F.283, F.286, P.287 Chain B: L.131, G.134, G.135, H.136, L.137, Y.141, S.192, A.193, N.374, N.376, A.384, R.391 Ligands: EDO.4, PLG.7 24 PLIP interactions: 17 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.137, B:Y.141, B:A.384, A:F.286 Hydrogen bonds: B:G.134, B:G.135, B:G.135, B:L.137, B:Y.141, B:S.192, B:N.374, B:N.376, B:N.376, B:L.385, A:E.63, A:Y.70, A:Y.70, A:Y.70, A:Y.71 Water bridges: B:K.147, B:K.147, B:A.384 Salt bridges: B:K.147 pi-Stacking: A:Y.70 FFO.14: 19 residues within 4Å: Chain C: L.131, G.134, G.135, H.136, L.137, Y.141, S.192, A.193, N.374, N.376, A.384 Chain D: E.63, Y.70, Y.71, F.283, F.286, P.287 Ligands: PLG.13, EDO.20 26 PLIP interactions: 20 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.137, C:Y.141, C:A.384, C:A.384, D:F.286 Hydrogen bonds: C:G.134, C:G.135, C:G.135, C:L.137, C:S.192, C:N.374, C:N.376, C:N.376, C:L.385, D:E.63, D:Y.70, D:Y.70, D:Y.70 Water bridges: C:K.147, C:K.147, C:K.147, C:A.384, C:A.384, C:A.384 Salt bridges: C:K.147 pi-Stacking: D:Y.70 FFO.23: 19 residues within 4Å: Chain C: E.63, Y.70, Y.71, F.283, F.286, P.287 Chain D: L.131, G.134, G.135, H.136, L.137, Y.141, S.192, A.193, N.374, N.376, A.384 Ligands: PLG.22, EDO.24 22 PLIP interactions: 17 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.137, D:Y.141, D:A.384, C:F.286 Hydrogen bonds: D:G.135, D:G.135, D:L.137, D:Y.141, D:S.192, D:N.374, D:N.376, D:N.376, D:L.385, C:E.63, C:Y.70, C:Y.70 Water bridges: D:K.147, D:K.147, D:K.147, D:A.384 Salt bridges: D:K.147 pi-Stacking: C:Y.70

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

EDO.3: 7 residues within 4Å: Chain A: K.375, A.384, L.385 Chain B: N.68, R.69, Y.70 Ligands: FFO.2 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: N.68, R.69, Y.70 Chain B: K.375, A.384, L.385 Ligands: FFO.8 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: R.125, F.182, R.183 Chain C: Y.142, K.148 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: I.50, E.51, G.54 Chain B: I.50, E.51, G.54 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain B: D.130, Y.142, T.143, S.144, P.160 Chain D: D.181 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: R.125, F.182, R.183 Chain D: Y.142, K.148 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: P.110, F.113, L.289 Chain B: P.110, F.113, L.289 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: D.130, Y.142, T.143, S.144, P.160 Chain C: L.180, D.181 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: Y.142, K.148 Chain C: R.125, F.182, R.183 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: L.180, D.181 Chain C: Y.142, T.143, S.144, P.160, K.162 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain C: P.110, F.113, L.289 Chain D: P.110, F.113, L.289 Ligand excluded by PLIP EDO.18: 1 residues within 4Å: Chain C: N.441 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: Y.142, K.148 Chain D: R.125, F.182, R.183 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain C: K.375, A.384, L.385 Chain D: N.68, R.69, Y.70 Ligands: FFO.14 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain C: I.50, E.51, G.54 Chain D: I.50, E.51, G.54 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: N.68, R.69, Y.70 Chain D: K.375, A.384, L.385 Ligands: FFO.23 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: D.181 Chain D: D.130, Y.142, T.143, S.144, P.160 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korasick, D.A. et al., Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to the soybean cyst nematode. J.Biol.Chem. (2020)

Release Date

2020-02-12

Peptides

Serine hydroxymethyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Serine hydroxymethyltransferase

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