- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.54 Å
- Oligo State
- homo-tetramer
- Ligands
- 3 x PLS: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE(Non-covalent)
- 38 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.2: 4 residues within 4Å:- Chain A: Q.89, L.93, G.104, V.105
Ligand excluded by PLIPEDO.3: 5 residues within 4Å:- Chain A: P.114, F.117, L.291
- Chain B: P.114, F.117
Ligand excluded by PLIPEDO.4: 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 PLIPEDO.5: 5 residues within 4Å:- Chain A: E.24, D.27, I.28, L.31
- Chain B: M.83
Ligand excluded by PLIPEDO.6: 3 residues within 4Å:- Chain A: E.472, K.473, E.474
Ligand excluded by PLIPEDO.7: 6 residues within 4Å:- Chain A: T.121, A.122, L.123, L.124, K.125, R.282
Ligand excluded by PLIPEDO.8: 5 residues within 4Å:- Chain A: Y.338, K.357, D.417, K.421, L.424
Ligand excluded by PLIPEDO.9: 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 PLIPEDO.11: 5 residues within 4Å:- Chain A: M.54, G.58
- Chain B: M.54, Q.55, G.58
Ligand excluded by PLIPEDO.13: 6 residues within 4Å:- Chain B: T.121, A.122, L.123, L.124, K.125, R.282
Ligand excluded by PLIPEDO.14: 4 residues within 4Å:- Chain B: Q.89, L.93, G.104, V.105
Ligand excluded by PLIPEDO.15: 5 residues within 4Å:- Chain B: Y.338, K.357, D.417, K.421, L.424
Ligand excluded by PLIPEDO.16: 5 residues within 4Å:- Chain A: M.83
- Chain B: E.24, D.27, I.28, L.31
Ligand excluded by PLIPEDO.17: 4 residues within 4Å:- Chain A: K.377
- Chain B: A.72, R.73, Y.74
Ligand excluded by PLIPEDO.18: 3 residues within 4Å:- Chain B: L.98, W.103, F.237
Ligand excluded by PLIPEDO.19: 8 residues within 4Å:- Chain B: I.130, A.132, D.134, H.143, G.144, T.161, M.162, P.163
Ligand excluded by PLIPEDO.20: 5 residues within 4Å:- Chain B: L.18, D.19, A.26, I.29, E.30
Ligand excluded by PLIPEDO.21: 1 residues within 4Å:- Chain B: F.466
Ligand excluded by PLIPEDO.23: 5 residues within 4Å:- Chain C: T.468, F.471, E.472, K.473, E.474
Ligand excluded by PLIPEDO.24: 4 residues within 4Å:- Chain C: K.102, W.103, F.237, R.262
Ligand excluded by PLIPEDO.25: 5 residues within 4Å:- Chain C: E.24, D.27, I.28, L.31
- Chain D: M.83
Ligand excluded by PLIPEDO.26: 3 residues within 4Å:- Chain C: K.434, L.435, K.436
Ligand excluded by PLIPEDO.27: 2 residues within 4Å:- Chain C: V.232, D.320
Ligand excluded by PLIPEDO.28: 4 residues within 4Å:- Chain C: R.199, G.343, T.345, D.346
Ligand excluded by PLIPEDO.30: 5 residues within 4Å:- Chain C: Y.338, K.357, D.417, K.421, L.424
Ligand excluded by PLIPEDO.31: 6 residues within 4Å:- Chain C: M.54, Q.55, G.58
- Chain D: M.54, Q.55, G.58
Ligand excluded by PLIPEDO.32: 5 residues within 4Å:- Chain C: A.122, L.123, L.124, K.125, R.282
Ligand excluded by PLIPEDO.33: 9 residues within 4Å:- Chain C: A.132, L.133, D.134, L.135, G.144, Y.145, T.161, M.162, P.163
Ligand excluded by PLIPEDO.35: 6 residues within 4Å:- Chain C: P.114, F.117, L.291
- Chain D: P.114, F.117, L.291
Ligand excluded by PLIPEDO.36: 7 residues within 4Å:- Chain C: K.150, K.151, I.152
- Chain D: Q.285, A.286, P.289, G.290
Ligand excluded by PLIPEDO.37: 7 residues within 4Å:- Chain C: Q.285, A.286, P.289, G.290
- Chain D: K.151, I.152, I.157
Ligand excluded by PLIPEDO.38: 4 residues within 4Å:- Chain D: Q.89, L.93, G.104, V.105
Ligand excluded by PLIPEDO.39: 3 residues within 4Å:- Chain D: W.103, F.237
- Ligands: EDO.44
Ligand excluded by PLIPEDO.40: 7 residues within 4Å:- Chain D: N.169, T.170, G.171, L.340, V.341, S.342, G.343
Ligand excluded by PLIPEDO.42: 6 residues within 4Å:- Chain D: T.121, A.122, L.123, L.124, K.125, R.282
Ligand excluded by PLIPEDO.43: 8 residues within 4Å:- Chain D: I.130, A.132, D.134, H.143, G.144, T.161, M.162, P.163
Ligand excluded by PLIPEDO.44: 7 residues within 4Å:- Chain D: R.207, Y.239, A.240, D.241, R.262, Y.277
- Ligands: EDO.39
Ligand excluded by PLIPEDO.45: 8 residues within 4Å:- Chain C: N.63, K.64
- Chain D: R.35, E.41, E.46, N.47, F.48, A.398
Ligand excluded by PLIP- 3 x LYA: 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID(Non-covalent)
LYA.10: 9 residues within 4Å:- Chain A: Y.74, F.288, P.289
- Chain B: L.135, L.141, T.147, K.150, I.152, M.387
14 PLIP interactions:11 interactions with chain B, 3 interactions with chain A- Hydrophobic interactions: B:L.141, B:I.152, A:Y.74, A:F.288, A:P.289
- Hydrogen bonds: B:L.135, B:T.147
- Water bridges: B:G.138, B:K.150, B:T.379, B:T.379, B:T.379, B:T.379
- Salt bridges: B:K.150
LYA.29: 10 residues within 4Å:- Chain C: L.135, L.141, Y.145, T.147, K.150, I.152, T.379, A.386, M.387
- Chain D: Y.74
15 PLIP interactions:14 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:L.135, C:L.141, C:Y.145, C:I.152, D:Y.74
- Hydrogen bonds: C:L.135, C:T.379, C:T.379, C:A.386
- Water bridges: C:G.138, C:T.149, C:K.150, C:K.150, C:T.379
- Salt bridges: C:K.150
LYA.41: 11 residues within 4Å:- Chain C: E.67, Y.74, F.288
- Chain D: L.135, L.141, Y.145, T.147, K.150, I.152, M.387
- Ligands: SER.34
14 PLIP interactions:4 Ligand-Ligand interactions, 8 interactions with chain D, 2 interactions with chain C- Hydrogen bonds: S.34, S.34, S.34, S.34, C:E.67
- Hydrophobic interactions: D:L.135, D:L.141, D:Y.145, D:I.152, C:Y.74
- Water bridges: D:T.149, D:T.149, D:K.150
- Salt bridges: D:K.150
- 1 x SER: SERINE(Non-covalent)
SER.34: 10 residues within 4Å:- Chain C: Y.65, E.67, Y.75
- Chain D: S.45, S.195, H.223, K.249, R.393
- Ligands: LYA.41, PLP.46
11 PLIP interactions:6 interactions with chain D, 2 Ligand-Ligand interactions, 3 interactions with chain C- Hydrogen bonds: D:S.45, D:S.195, D:R.393, S.34, C:E.67, C:Y.75, C:Y.75
- Salt bridges: D:H.223, D:K.249, D:R.393
- Water bridges: S.34
- 1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)
PLP.46: 17 residues within 4Å:- Chain C: Y.65, G.293, G.294
- Chain D: 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
- Ligands: SER.34
18 PLIP interactions:4 interactions with chain C, 14 interactions with chain D- Hydrogen bonds: C:Y.65, C:G.293, C:G.294, D:G.112, D:S.113, D:N.116, D:S.142, D:S.195, D:K.249
- Water bridges: C:Y.65, D:S.111, D:S.111, D:S.111, D:T.246
- Hydrophobic interactions: D:K.249
- Salt bridges: D:H.248, D:K.249
- pi-Stacking: D:H.140
- 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
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.54 Å
- Oligo State
- homo-tetramer
- Ligands
- 3 x PLS: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE(Non-covalent)
- 38 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x LYA: 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID(Non-covalent)
- 1 x SER: SERINE(Non-covalent)
- 1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)
- 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
AB
BC
CD
D