SMTL ID : 6smn.1

A. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) in complex with methotrexate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-tetramer

Ligands

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

PLS.1: 21 residues within 4Å: Chain A: S.45, S.111, G.112, S.113, H.140, S.142, A.194, S.195, D.220, A.222, H.223, T.246, H.248, K.249, R.393 Chain B: Y.65, E.67, Y.75, G.293, G.294 Ligands: EDO.5 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.222 Hydrogen bonds: A:S.45, A:G.112, A:S.113, A:S.195, A:S.195, A:K.249, B:Y.65, B:E.67, B:Y.75, B:G.293, B:G.294 Water bridges: A:S.111, A:S.111, A:R.255 Salt bridges: A:H.223, A:H.248, A:K.249, A:R.393 pi-Stacking: A:H.140 PLS.19: 20 residues within 4Å: Chain A: Y.65, E.67, Y.75, G.293, G.294 Chain B: S.45, S.111, G.112, S.113, H.140, S.142, A.194, S.195, D.220, A.222, H.223, T.246, H.248, K.249, R.393 23 PLIP interactions: 17 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.222 Hydrogen bonds: B:S.45, B:G.112, B:S.113, B:S.113, B:S.195, A:Y.65, A:E.67, A:Y.75, A:Y.75, A:G.293, A:G.294 Water bridges: B:S.111, B:S.111, B:T.244, B:R.255, B:R.393, B:R.393 Salt bridges: B:H.223, B:H.248, B:K.249, B:R.393 pi-Stacking: B:H.140 PLS.30: 20 residues within 4Å: Chain C: S.45, S.111, G.112, S.113, H.140, S.142, A.194, S.195, D.220, A.222, H.223, T.246, H.248, K.249, R.393 Chain D: Y.65, E.67, Y.75, G.293, G.294 24 PLIP interactions: 18 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:A.222 Hydrogen bonds: C:S.45, C:G.112, C:S.113, C:S.113, C:S.195, C:K.249, D:Y.65, D:E.67, D:Y.75, D:Y.75, D:G.293, D:G.294 Water bridges: C:S.111, C:S.111, C:T.244, C:R.255, C:R.393, C:R.393 Salt bridges: C:H.223, C:H.248, C:K.249, C:R.393 pi-Stacking: C:H.140

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

EDO.2: 10 residues within 4Å: Chain A: I.130, A.132, L.133, D.134, L.135, H.143, G.144, T.161, M.162, P.163 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: Q.89, L.93, G.104, V.105 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: L.135, G.139, H.140, L.141, S.195 Ligands: PLS.1, MTX.3 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: P.114, F.117, L.291 Chain B: P.114, F.117 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: P.467, T.468, F.471, E.472, K.473 Chain B: N.15 Ligands: EDO.10 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: T.121, A.122, L.123, L.124, K.125, R.282 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: E.24, D.27, I.28, L.31 Chain B: M.83 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: E.472, K.473, E.474 Ligands: EDO.7 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: A.72, R.73, Y.74 Chain B: K.377 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: I.173, D.174, Y.175, D.176 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: R.311, T.312, P.313, K.316 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: L.18, D.19, A.26, I.29, E.30 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: A.386, M.387 Chain B: Y.74 Ligands: MTX.3 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: K.377 Chain B: A.72, R.73, Y.74 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: K.151, I.152, I.157 Chain B: Q.285, A.286, P.289, G.290 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: Q.285, A.286, P.289, G.290 Chain B: K.151, I.152, I.157 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain B: A.132, L.133, D.134, L.135, H.143, G.144, T.161, M.162, P.163 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: Q.89, L.93, G.104, V.105 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: Y.338, K.357, D.417, K.421, L.424 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: M.83 Chain B: E.24, D.27, I.28, L.31 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: L.98, W.103, F.237 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: T.121, A.122, L.123, L.124, K.125, R.282 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: I.173, D.174, Y.175, D.176 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: Q.97, L.98, D.99 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain B: Q.465, F.466 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain C: I.130, A.132, D.134, H.143, G.144, T.161, M.162, P.163 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain C: W.103, F.237, R.262 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain C: E.24, D.27, I.28, L.31 Chain D: M.83 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain C: K.434, L.435, K.436 Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Chain C: V.232, D.320 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain C: R.199, G.343, T.345 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain C: P.114, F.117, L.291 Chain D: P.114, F.117, L.291 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain C: Y.338, K.357, D.417, K.421, L.424 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain C: D.408, Y.462, Q.465 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain C: M.54, Q.55, G.58 Chain D: M.54, Q.55, G.58 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain C: T.468, E.472, K.473, E.474 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain C: T.121, A.122, L.123, L.124, K.125, R.282 Ligand excluded by PLIP EDO.44: 2 residues within 4Å: Chain C: R.7 Chain D: P.467 Ligand excluded by PLIP EDO.45: 8 residues within 4Å: Chain C: Q.285, A.286, P.289, G.290 Chain D: K.150, K.151, I.152, I.157 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain C: K.151, I.152, I.157 Chain D: Q.285, A.286, P.289, G.290 Ligand excluded by PLIP EDO.48: 8 residues within 4Å: Chain D: A.132, L.133, D.134, H.143, G.144, T.161, M.162, P.163 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain D: Q.89, L.93, G.104, V.105 Ligand excluded by PLIP EDO.51: 2 residues within 4Å: Chain D: W.103, F.237 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain D: N.169, T.170, G.171, L.340, V.341, S.342, G.343 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain D: A.34, K.38, Y.478, E.480 Ligand excluded by PLIP EDO.54: 6 residues within 4Å: Chain D: R.207, Y.239, A.240, D.241, R.262, Y.277 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain D: T.121, A.122, L.123, L.124, K.125, R.282 Ligand excluded by PLIP EDO.56: 9 residues within 4Å: Chain C: N.63, K.64 Chain D: R.35, Q.36, E.41, E.46, N.47, F.48, A.398 Ligand excluded by PLIP

4 x MTX: METHOTREXATE(Non-covalent)

MTX.3: 14 residues within 4Å: Chain A: L.141, Y.145, T.147, D.148, T.149, I.152, N.376, K.377, A.386 Chain B: E.67, Y.74, F.288 Ligands: EDO.5, EDO.15 14 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:E.67, B:E.67, A:Y.145, A:Y.145, A:T.147, A:D.148, A:T.149, A:N.376, A:K.377 pi-Stacking: B:Y.74 Hydrophobic interactions: A:Y.145, A:A.386 Water bridges: A:T.379, D:R.186 MTX.21: 14 residues within 4Å: Chain A: E.67, Y.74, P.289 Chain B: L.135, L.141, Y.145, T.147, D.148, T.149, I.152, N.376, K.377, A.386, M.387 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.145, B:A.386 Hydrogen bonds: B:Y.145, B:Y.145, B:Y.145, B:T.147, B:D.148, B:T.149, B:N.376, B:K.377, A:E.67 Water bridges: B:T.147, B:T.379 MTX.32: 12 residues within 4Å: Chain C: L.141, Y.145, T.147, D.148, T.149, I.152, N.376, K.377, A.386 Chain D: E.67, Y.74, F.288 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.145, C:A.386 Hydrogen bonds: C:Y.145, C:T.147, C:D.148, C:D.148, C:D.148, C:T.149, C:N.376, C:K.377, D:E.67 Water bridges: C:T.379 MTX.46: 10 residues within 4Å: Chain A: R.186 Chain C: Y.74 Chain D: L.135, Y.145, T.147, D.148, I.152, K.377, S.385, M.387 9 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:T.147 Hydrogen bonds: D:D.148, D:K.377, C:Y.74 Water bridges: D:T.149 pi-Stacking: D:Y.145, C:Y.74, C:Y.74 Salt bridges: A:R.186

1 x SER: SERINE(Non-covalent)

SER.49: 8 residues within 4Å: Chain C: Y.65, E.67, Y.75 Chain D: S.45, S.195, H.223, K.249, R.393 9 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: D:S.45, C:E.67, C:Y.75, C:Y.75, S.49 Water bridges: D:S.195, S.49 Salt bridges: D:H.223, D:R.393

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 2, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Serine hydroxymethyltransferase 2, mitochondrial

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