SMTL ID : 6cd0.1

Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), PLP-internal aldimine and apo form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

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

ACT.1: 9 residues within 4Å: Chain A: S.36, H.131, S.186, H.214, K.240, R.376 Chain B: Y.56, E.58, Y.66 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.36, B:Y.66 Salt bridges: A:H.214, A:R.376 ACT.3: 8 residues within 4Å: Chain A: E.58, Y.66 Chain B: S.36, H.131, S.186, H.214, K.240, R.376 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.36, B:S.186 Salt bridges: B:H.214, B:R.376 ACT.5: 6 residues within 4Å: Chain C: S.102, G.103, S.104, T.237 Chain D: G.276 Ligands: FMT.6 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:T.237 Hydrogen bonds: C:S.102, C:G.103, C:S.104, D:G.276, D:G.277 Salt bridges: C:K.240

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 8 residues within 4Å: Chain B: A.213, S.216, T.237, T.238, H.239, K.240, S.241, L.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.216, B:L.242 FMT.4: 9 residues within 4Å: Chain C: A.213, S.216, T.236, T.237, T.238, H.239, K.240, S.241, L.242 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.216, C:T.237, C:T.237, C:H.239, C:K.240, C:S.241, C:L.242 FMT.6: 7 residues within 4Å: Chain C: S.102 Chain D: L.101, Q.275, G.276, G.277, H.279 Ligands: ACT.5 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.275, D:G.276, C:S.102, C:S.102 FMT.7: 9 residues within 4Å: Chain D: A.213, S.216, T.236, T.237, T.238, H.239, K.240, S.241, L.242 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.216, D:T.238, D:S.241, D:L.242

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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