SMTL ID : 6smr.1

A. thaliana serine hydroxymethyltransferase isoform 4 (AtSHMT4) in complex with methotrexate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-tetramer

Ligands

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

PLS.1: 20 residues within 4Å: Chain A: S.42, S.108, G.109, S.110, N.113, H.137, G.192, S.193, D.218, A.220, H.221, T.244, H.246, K.247, R.392 Chain B: Y.62, E.64, Y.107, G.292, G.293 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.220 Hydrogen bonds: A:S.42, A:G.109, A:S.110, A:N.113, A:S.193, A:S.193, A:K.247, B:Y.62, B:E.64, B:G.292, B:G.293 Water bridges: A:S.108, A:S.108, A:S.193, A:S.193 Salt bridges: A:H.221, A:H.246, A:K.247, A:R.392 pi-Stacking: A:H.137 PLS.6: 21 residues within 4Å: Chain A: Y.62, E.64, Y.72, Y.107, G.292, G.293 Chain B: S.42, S.108, G.109, S.110, N.113, H.137, G.192, S.193, D.218, A.220, H.221, T.244, H.246, K.247, R.392 23 PLIP interactions: 18 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:H.137, B:A.220 Hydrogen bonds: B:S.42, B:G.109, B:S.110, B:S.110, B:N.113, B:S.193, B:S.193, B:K.247, A:Y.62, A:E.64, A:Y.72, A:G.292, A:G.293 Water bridges: B:S.108, B:T.242, B:R.253 Salt bridges: B:H.221, B:H.246, B:K.247, B:R.392 pi-Stacking: B:H.137 PLS.10: 21 residues within 4Å: Chain C: S.42, S.108, G.109, S.110, N.113, H.137, G.192, S.193, D.218, A.220, H.221, T.244, H.246, K.247, R.392 Chain D: Y.62, E.64, Y.72, Y.107, G.292, G.293 19 PLIP interactions: 14 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:A.220 Hydrogen bonds: C:S.42, C:G.109, C:S.110, C:S.110, C:N.113, C:S.193, D:Y.62, D:E.64, D:Y.107, D:G.292, D:G.293 Water bridges: C:S.108, C:S.108 Salt bridges: C:H.221, C:H.246, C:K.247, C:R.392 pi-Stacking: C:H.137 PLS.15: 20 residues within 4Å: Chain C: Y.62, E.64, Y.107, G.292, G.293 Chain D: S.42, S.108, G.109, S.110, N.113, H.137, G.192, S.193, D.218, A.220, H.221, T.244, H.246, K.247, R.392 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:A.220 Hydrogen bonds: D:S.42, D:G.109, D:S.110, D:N.113, D:K.247, C:Y.62, C:E.64, C:Y.107, C:G.292, C:G.293 Water bridges: D:S.108, D:R.253 Salt bridges: D:H.221, D:H.246, D:K.247, D:R.392 pi-Stacking: D:H.137

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

EDO.2: 6 residues within 4Å: Chain A: R.126, F.183, R.184, K.186 Chain D: G.147, K.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.184 EDO.4: 7 residues within 4Å: Chain A: A.289, L.290 Chain B: S.110, N.113, F.114, T.139, T.153 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.114, A:L.290 EDO.7: 6 residues within 4Å: Chain A: I.51, E.52, G.55 Chain B: I.51, E.52, G.55 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.52 EDO.8: 4 residues within 4Å: Chain B: K.179, D.182 Chain C: L.160, D.182 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.179, C:D.182, C:D.182, B:K.179, B:D.182 EDO.9: 4 residues within 4Å: Chain A: S.56 Chain B: H.23, I.26, E.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.23, B:E.27 EDO.11: 7 residues within 4Å: Chain C: L.15, H.23, I.26, E.27, K.30 Chain D: E.52, S.56 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.23, C:E.27, C:K.30 EDO.13: 6 residues within 4Å: Chain C: I.51, E.52, G.55 Chain D: I.51, E.52, G.55 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.51 EDO.14: 6 residues within 4Å: Chain A: L.160, K.179, D.182 Chain D: L.160, K.179, D.182 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:K.179, A:D.182, D:D.182, D:D.182 EDO.17: 8 residues within 4Å: Chain D: G.192, S.193, A.194, Y.195, W.199, I.222, N.346, L.348 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.192, D:S.193, D:Y.195, D:W.199 Water bridges: D:N.346

3 x MTX: METHOTREXATE(Non-covalent)

MTX.3: 9 residues within 4Å: Chain A: Y.71, P.288 Chain B: Y.142, T.144, I.150, K.376, S.384, A.385, L.386 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.142, B:T.144 Hydrogen bonds: B:K.376, A:Y.71 pi-Stacking: A:Y.71, A:Y.71 pi-Cation interactions: A:Y.71 MTX.5: 13 residues within 4Å: Chain A: L.138, Y.142, T.144, S.145, G.146, I.150, K.376, S.383, A.385, L.386 Chain B: R.70, Y.71, P.288 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:Y.71, A:T.144, A:G.146, A:K.376, A:K.376, A:A.385 pi-Stacking: B:Y.71, B:Y.71 pi-Cation interactions: B:Y.71 Hydrophobic interactions: A:Y.142, A:T.144, A:I.150, A:A.385 MTX.16: 12 residues within 4Å: Chain C: R.70, Y.71 Chain D: Y.142, T.144, S.145, G.146, I.150, K.376, S.383, S.384, A.385, L.386 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.142, D:I.150, D:A.385 Hydrogen bonds: D:S.145, D:G.146, D:K.376, D:K.376, D:A.385 pi-Stacking: C:Y.71, C:Y.71 pi-Cation interactions: C:Y.71

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 4 residues within 4Å: Chain C: R.197, V.326, G.343, T.344 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.197, C:R.197, C:T.344 Water bridges: C:N.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruszkowski, M. et al., Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models. Sci Rep (2019)

Release Date

2020-01-08

Peptides

Serine hydroxymethyltransferase 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Serine hydroxymethyltransferase 4

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