SMTL ID : 6cd1.1 (1 other biounit)

Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), complexes with reaction intermediates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-tetramer

Ligands

2 x PLS: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE(Non-covalent)

PLS.1: 19 residues within 4Å: Chain A: S.36, S.102, G.103, S.104, H.131, A.185, S.186, D.211, A.213, H.214, T.237, H.239, K.240, R.376 Chain B: Y.56, E.58, Y.66, G.276, G.277 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.213 Hydrogen bonds: A:S.36, A:G.103, A:S.104, A:K.240, B:Y.56, B:E.58, B:Y.66, B:Y.66, B:G.276, B:G.277 Water bridges: A:S.102, A:S.102, A:N.107, A:S.186, A:R.246 Salt bridges: A:H.214, A:H.239, A:K.240, A:R.376 pi-Stacking: A:H.131 PLS.8: 20 residues within 4Å: Chain C: Y.56, E.58, Y.66, G.276, G.277 Chain D: S.36, S.102, G.103, S.104, N.107, H.131, A.185, S.186, D.211, A.213, H.214, T.237, H.239, K.240, R.376 23 PLIP interactions: 17 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:A.213 Hydrogen bonds: D:S.36, D:G.103, D:S.104, D:S.104, D:N.107, D:S.186, D:S.186, D:K.240, C:Y.56, C:Y.66, C:G.276, C:G.277 Water bridges: D:S.102, D:S.102, D:R.246, C:E.58, C:E.58 Salt bridges: D:H.214, D:H.239, D:K.240, D:R.376 pi-Stacking: D:H.131

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

EDO.2: 4 residues within 4Å: Chain A: Q.80, L.84, G.95, V.96 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.96, A:V.96 Water bridges: A:K.254, A:K.254 EDO.4: 5 residues within 4Å: Chain B: Q.80, Q.81, L.84, G.95, V.96 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.81, B:V.96, B:V.96, B:E.263 Water bridges: B:Q.81 EDO.7: 5 residues within 4Å: Chain C: Q.80, Q.81, L.84, G.95, V.96 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.81, C:V.96, C:E.263 Water bridges: C:K.254 EDO.9: 5 residues within 4Å: Chain D: Q.80, Q.81, L.84, G.95, V.96 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.81, D:V.96, D:V.96 Water bridges: D:K.254

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

PLG.3: 20 residues within 4Å: Chain A: Y.56, E.58, Y.66, G.276, G.277 Chain B: S.36, S.102, G.103, S.104, N.107, H.131, A.185, S.186, D.211, A.213, H.214, T.237, H.239, K.240, R.376 19 PLIP interactions: 4 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:Y.56, A:Y.66, A:G.276, A:G.277, B:S.36, B:S.102, B:G.103, B:S.104, B:S.186, B:K.240 Hydrophobic interactions: B:A.213 Water bridges: B:S.102, B:N.107, B:R.246 Salt bridges: B:H.214, B:H.239, B:K.240, B:R.376 pi-Stacking: B:H.131

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 7 residues within 4Å: Chain C: S.102, G.103, S.104, T.237 Chain D: Y.56, G.276, G.277 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.103, C:S.104, D:G.276 Water bridges: C:S.102, C:S.102 Salt bridges: C:H.239, C:K.240 Hydrophobic interactions: D:Y.56 ACT.6: 7 residues within 4Å: Chain C: S.36, S.186, H.214, K.240, R.376 Chain D: E.58, Y.66 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.36, D:Y.66 Salt bridges: C:H.214, C:K.240, C:R.376

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruszkowski, M. et al., Chloroplastic Serine Hydroxymethyltransferase FromMedicago truncatula: A Structural Characterization. Front Plant Sci (2018)

Release Date

2018-05-23

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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