SMTL ID : 6ccz.1

Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3) soaked with selenourea

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

38 x SEY: selenourea(Non-covalent)

SEY.1: 4 residues within 4Å: Chain A: P.105, F.108 Chain C: L.274 Ligands: SEY.25 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.274 Water bridges: C:Q.275 SEY.2: 3 residues within 4Å: Chain A: D.297, N.300, Y.301 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.297, A:N.300 Water bridges: A:R.243 SEY.3: 6 residues within 4Å: Chain A: Q.80, G.95, V.96, K.254, E.263 Ligands: SEY.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.96, A:V.96, A:E.263 Water bridges: A:Q.80, A:K.254, A:K.254 SEY.4: 4 residues within 4Å: Chain A: Y.292, S.295, P.296, D.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.295, A:S.295 SEY.5: 7 residues within 4Å: Chain A: G.184, A.185, Y.188, R.190, M.210, V.215, N.330 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.185, A:Y.188, A:Y.188, A:N.330 SEY.6: 5 residues within 4Å: Chain A: L.60, P.61, I.77, Q.80 Ligands: SEY.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.80, A:Q.80 SEY.7: 6 residues within 4Å: Chain A: G.59, L.60, N.267, N.268, F.271, P.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.267 Water bridges: A:N.267 SEY.8: 5 residues within 4Å: Chain A: P.117, H.118 Chain B: H.118 Chain C: H.118 Chain D: P.117 No protein-ligand interaction detected (PLIP) SEY.9: 5 residues within 4Å: Chain A: P.451, I.452, P.453 Chain C: F.4, D.6 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:F.4, C:D.6, A:I.452 SEY.10: 2 residues within 4Å: Chain A: R.29, T.448 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.448, A:T.448 SEY.11: 5 residues within 4Å: Chain A: S.41, V.288, Y.292 Chain C: L.5, A.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.5 SEY.14: 7 residues within 4Å: Chain B: G.184, A.185, Y.188, R.190, M.210, V.215, N.330 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.185, B:Y.188, B:Y.188, B:N.330 SEY.15: 4 residues within 4Å: Chain B: L.274 Chain D: P.105, F.108 Ligands: SEY.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.274 SEY.16: 3 residues within 4Å: Chain B: L.412, V.413, S.414 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.412, B:S.414 SEY.17: 5 residues within 4Å: Chain B: Q.80, G.95, V.96, K.254, E.263 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.96, B:V.96, B:K.254, B:K.254 Water bridges: B:N.267 SEY.18: 7 residues within 4Å: Chain B: T.384, P.451, I.452, P.453 Chain D: F.4, L.5, D.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:I.452, D:F.4 SEY.19: 4 residues within 4Å: Chain B: V.317, K.322, L.323, G.326 No protein-ligand interaction detected (PLIP) SEY.20: 5 residues within 4Å: Chain B: S.41, V.288, Y.292 Chain D: L.5, A.12 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Y.7 Water bridges: D:L.5, D:D.6, D:D.6, B:S.41 SEY.21: 4 residues within 4Å: Chain B: G.62, R.64, Y.66 Chain D: E.348 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.64, B:Y.66 Water bridges: B:E.70, D:E.348, D:E.348 SEY.25: 4 residues within 4Å: Chain A: L.274 Chain C: P.105, F.108 Ligands: SEY.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.274 Water bridges: A:Q.275 SEY.26: 3 residues within 4Å: Chain C: D.297, N.300, Y.301 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:F.4, C:D.297, C:N.300 Water bridges: C:R.243 SEY.27: 6 residues within 4Å: Chain C: Q.80, G.95, V.96, K.254, E.263 Ligands: SEY.30 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.96, C:V.96 Water bridges: C:Q.80, C:K.254, C:K.254 SEY.28: 4 residues within 4Å: Chain C: Y.292, S.295, P.296, D.297 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.295, C:S.295 SEY.29: 7 residues within 4Å: Chain C: G.184, A.185, Y.188, R.190, M.210, V.215, N.330 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.185, C:Y.188, C:Y.188, C:N.330 SEY.30: 5 residues within 4Å: Chain C: L.60, P.61, I.77, Q.80 Ligands: SEY.27 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.80, C:Q.80 SEY.31: 6 residues within 4Å: Chain C: G.59, L.60, N.267, N.268, F.271, P.272 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.267 Water bridges: C:N.267 SEY.32: 5 residues within 4Å: Chain A: H.118 Chain B: P.117 Chain C: P.117, H.118 Chain D: H.118 No protein-ligand interaction detected (PLIP) SEY.33: 5 residues within 4Å: Chain A: F.4, D.6 Chain C: P.451, I.452, P.453 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:I.452, A:F.4 SEY.34: 2 residues within 4Å: Chain C: R.29, T.448 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.448 SEY.35: 5 residues within 4Å: Chain A: L.5, A.12 Chain C: S.41, V.288, Y.292 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.5 SEY.38: 7 residues within 4Å: Chain D: G.184, A.185, Y.188, R.190, M.210, V.215, N.330 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.185, D:Y.188, D:Y.188, D:N.330 SEY.39: 4 residues within 4Å: Chain B: P.105, F.108 Chain D: L.274 Ligands: SEY.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.274 SEY.40: 3 residues within 4Å: Chain D: L.412, V.413, S.414 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.412, D:S.414 SEY.41: 5 residues within 4Å: Chain D: Q.80, G.95, V.96, K.254, E.263 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:V.96, D:V.96, D:K.254, D:K.254, D:E.263 Water bridges: D:N.267 SEY.42: 7 residues within 4Å: Chain B: F.4, L.5, D.6 Chain D: T.384, P.451, I.452, P.453 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:I.452, B:F.4 SEY.43: 4 residues within 4Å: Chain D: V.317, K.322, L.323, G.326 No protein-ligand interaction detected (PLIP) SEY.44: 5 residues within 4Å: Chain B: L.5, A.12 Chain D: S.41, V.288, Y.292 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.7 Water bridges: B:L.5, B:D.6, B:D.6, D:S.41 SEY.45: 4 residues within 4Å: Chain B: E.348 Chain D: G.62, R.64, Y.66 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.64, D:Y.66 Water bridges: D:E.70

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

ACT.12: 9 residues within 4Å: Chain A: S.36, H.131, S.186, H.214, K.240, R.376 Chain C: Y.56, E.58, Y.66 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.36, A:S.186 Salt bridges: A:H.214, A:R.376 Hydrophobic interactions: C:Y.56 ACT.22: 9 residues within 4Å: Chain B: S.36, H.131, S.186, H.214, K.240, R.376 Chain D: Y.56, E.58, Y.66 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.36, D:Y.66 Water bridges: B:K.240 Salt bridges: B:H.214, B:K.240, B:R.376 ACT.23: 8 residues within 4Å: Chain B: S.102, G.103, S.104, H.131, T.237 Chain D: Y.56, G.276, G.277 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:T.237 Hydrogen bonds: B:S.102, B:G.103, B:S.104, B:H.239, D:G.276, D:G.277 Salt bridges: B:K.240 ACT.36: 9 residues within 4Å: Chain A: Y.56, E.58, Y.66 Chain C: S.36, H.131, S.186, H.214, K.240, R.376 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.36, C:S.186, A:Y.66 Salt bridges: C:H.214, C:R.376 Hydrophobic interactions: A:Y.56 ACT.46: 9 residues within 4Å: Chain B: Y.56, E.58, Y.66 Chain D: S.36, H.131, S.186, H.214, K.240, R.376 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:S.36, B:Y.66, B:Y.66 Water bridges: D:K.240 Salt bridges: D:H.214, D:K.240, D:R.376 ACT.47: 8 residues within 4Å: Chain B: Y.56, G.276, G.277 Chain D: S.102, G.103, S.104, H.131, T.237 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:T.237 Hydrogen bonds: D:S.102, D:G.103, D:S.104, D:H.239, B:Y.56, B:G.276, B:G.277 Salt bridges: D:K.240

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

FMT.13: 9 residues within 4Å: Chain A: A.213, S.216, T.236, T.237, T.238, H.239, K.240, S.241, L.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.237, A:T.237, A:H.239, A:S.241, A:L.242 FMT.24: 9 residues within 4Å: Chain B: A.213, S.216, T.236, T.237, T.238, H.239, K.240, S.241, L.242 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.216, B:H.239, B:K.240, B:S.241, B:L.242 FMT.37: 9 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:T.237, C:H.239, C:S.241, C:L.242 FMT.48: 9 residues within 4Å: Chain D: A.213, S.216, T.236, T.237, T.238, H.239, K.240, S.241, L.242 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.216, D:T.237, D:H.239, D:K.240, 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
A

D
B

Serine hydroxymethyltransferase

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