SMTL ID : 6uxi.1

Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP-Glycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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: 19 residues within 4Å: Chain A: S.41, S.107, G.108, S.109, H.136, G.191, S.192, D.217, A.219, H.220, T.243, H.245, K.246, R.391 Chain B: Y.61, E.63, Y.106, G.291, G.292 22 PLIP interactions: 6 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:Y.61, B:Y.61, B:E.63, B:Y.106, B:G.291, B:G.292, A:S.41, A:G.108, A:S.109, A:S.109, A:S.192, A:H.220, A:K.246 Hydrophobic interactions: A:A.219 Water bridges: A:S.107, A:N.112, A:R.252 Salt bridges: A:H.220, A:H.245, A:K.246, A:R.391 pi-Stacking: A:H.136 PLG.3: 19 residues within 4Å: Chain A: Y.61, E.63, Y.106, G.291, G.292 Chain B: S.41, S.107, G.108, S.109, H.136, G.191, S.192, D.217, A.219, H.220, T.243, H.245, K.246, R.391 22 PLIP interactions: 16 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.219 Hydrogen bonds: B:S.41, B:G.108, B:S.109, B:S.109, B:S.192, B:H.220, B:K.246, A:Y.61, A:Y.61, A:E.63, A:Y.106, A:G.291, A:G.292 Water bridges: B:S.107, B:N.112, B:R.252 Salt bridges: B:H.220, B:H.245, B:K.246, B:R.391 pi-Stacking: B:H.136 PLG.5: 19 residues within 4Å: Chain C: S.41, S.107, G.108, S.109, H.136, G.191, S.192, D.217, A.219, H.220, T.243, H.245, K.246, R.391 Chain D: Y.61, E.63, Y.106, G.291, G.292 20 PLIP interactions: 16 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:A.219 Hydrogen bonds: C:S.41, C:G.108, C:S.109, C:S.109, C:S.192, C:H.220, C:K.246, D:Y.61, D:E.63, D:G.291, D:G.292 Water bridges: C:S.107, C:N.112, C:R.252 Salt bridges: C:H.220, C:H.245, C:K.246, C:R.391 pi-Stacking: C:H.136 PLG.7: 19 residues within 4Å: Chain C: Y.61, E.63, Y.106, G.291, G.292 Chain D: S.41, S.107, G.108, S.109, H.136, G.191, S.192, D.217, A.219, H.220, T.243, H.245, K.246, R.391 20 PLIP interactions: 16 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:A.219 Hydrogen bonds: D:S.41, D:G.108, D:S.109, D:S.109, D:S.192, D:H.220, D:K.246, C:Y.61, C:E.63, C:G.291, C:G.292 Water bridges: D:S.107, D:T.241, D:R.252 Salt bridges: D:H.220, D:H.245, D:K.246, D:R.391 pi-Stacking: D:H.136

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

EDO.2: 6 residues within 4Å: Chain A: I.50, E.51, G.54 Chain B: I.50, E.51, G.54 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.51 EDO.4: 5 residues within 4Å: Chain B: K.178, D.181 Chain C: L.159, K.178, D.181 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.181, B:D.181, C:D.181 EDO.6: 6 residues within 4Å: Chain C: I.50, E.51, G.54 Chain D: I.50, E.51, G.54 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: L.159, K.178, D.181 Chain D: K.178, D.181 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:D.181, A:D.181, D:D.181

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
A

D
B

Serine hydroxymethyltransferase

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