- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.63 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)
- 4 x FFO: N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid(Non-covalent)
FFO.2: 20 residues within 4Å:- Chain A: L.149, G.152, G.153, H.154, L.155, Y.159, S.210, A.211, N.392, N.394, A.402, R.409
- Chain B: E.81, Y.88, Y.89, F.301, F.304, P.305
- Ligands: PLG.1, EDO.9
22 PLIP interactions:16 interactions with chain A, 6 interactions with chain B- Hydrophobic interactions: A:L.155, A:Y.159, A:A.402, A:A.402, B:Y.88, B:F.304
- Hydrogen bonds: A:G.152, A:G.153, A:G.153, A:L.155, A:Y.159, A:S.210, A:N.392, A:N.394, A:N.394, B:E.81, B:Y.88, B:Y.88, B:Y.88
- Water bridges: A:K.165, A:A.402
- Salt bridges: A:K.165
FFO.11: 20 residues within 4Å:- Chain A: E.81, Y.88, Y.89, F.301, F.304, P.305
- Chain B: L.149, G.152, G.153, H.154, L.155, Y.159, K.165, I.167, S.210, A.211, N.392, N.394
- Ligands: EDO.5, PLG.10
17 PLIP interactions:12 interactions with chain B, 5 interactions with chain A- Hydrophobic interactions: B:L.155, B:Y.159, A:Y.88, A:F.304
- Hydrogen bonds: B:G.153, B:G.153, B:L.155, B:Y.159, B:S.210, B:N.392, B:N.394, B:N.394, A:Y.88, A:Y.88, A:Y.88
- Water bridges: B:K.165
- Salt bridges: B:K.165
FFO.17: 19 residues within 4Å:- Chain C: L.149, G.152, G.153, H.154, L.155, Y.159, S.210, A.211, N.392, N.394, A.402
- Chain D: E.81, Y.88, Y.89, F.301, F.304, P.305
- Ligands: PLG.16, EDO.24
24 PLIP interactions:6 interactions with chain D, 18 interactions with chain C- Hydrophobic interactions: D:Y.88, D:F.304, C:L.155, C:Y.159, C:A.402, C:A.402
- Hydrogen bonds: D:E.81, D:Y.88, D:Y.88, D:Y.88, C:G.152, C:G.153, C:G.153, C:L.155, C:S.210, C:N.392, C:N.394, C:N.394, C:A.402, C:L.403
- Water bridges: C:K.165, C:K.165, C:K.165
- Salt bridges: C:K.165
FFO.22: 22 residues within 4Å:- Chain C: E.81, Y.88, Y.89, F.301, F.304, P.305
- Chain D: L.149, G.152, G.153, H.154, L.155, Y.159, K.165, I.167, S.210, A.211, N.392, N.394, A.402, R.409
- Ligands: PLG.21, EDO.23
19 PLIP interactions:14 interactions with chain D, 5 interactions with chain C- Hydrophobic interactions: D:L.155, D:Y.159, D:A.402, D:A.402, C:F.304
- Hydrogen bonds: D:G.153, D:G.153, D:L.155, D:S.210, D:N.392, D:N.394, D:N.394, C:Y.88, C:Y.88, C:Y.88
- Water bridges: D:K.165, D:A.402
- Salt bridges: D:K.165
- pi-Stacking: C:Y.88
- 18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 6 residues within 4Å:- Chain A: I.68, E.69, G.72
- Chain B: I.68, E.69, G.72
Ligand excluded by PLIPEDO.4: 5 residues within 4Å:- Chain A: R.143, F.200, R.201
- Chain C: Y.160, K.166
Ligand excluded by PLIPEDO.5: 5 residues within 4Å:- Chain A: N.86, R.87, Y.88
- Chain B: K.393
- Ligands: FFO.11
Ligand excluded by PLIPEDO.6: 6 residues within 4Å:- Chain A: Y.160, S.162, P.178, K.180
- Chain C: L.198, D.199
Ligand excluded by PLIPEDO.7: 8 residues within 4Å:- Chain A: L.198, D.199
- Chain C: D.148, Y.160, T.161, S.162, P.178, K.180
Ligand excluded by PLIPEDO.8: 6 residues within 4Å:- Chain A: P.128, F.131, L.307
- Chain B: P.128, F.131, L.307
Ligand excluded by PLIPEDO.9: 7 residues within 4Å:- Chain A: K.393, A.402, L.403
- Chain B: N.86, R.87, Y.88
- Ligands: FFO.2
Ligand excluded by PLIPEDO.12: 6 residues within 4Å:- Chain B: R.143, F.200, R.201
- Chain D: Y.160, G.164, K.166
Ligand excluded by PLIPEDO.13: 6 residues within 4Å:- Chain B: L.198, D.199
- Chain D: Y.160, S.162, P.178, K.180
Ligand excluded by PLIPEDO.14: 4 residues within 4Å:- Chain B: G.419, V.421, D.424, F.477
Ligand excluded by PLIPEDO.15: 6 residues within 4Å:- Chain B: D.148, Y.160, T.161, S.162, P.178
- Chain D: D.199
Ligand excluded by PLIPEDO.18: 5 residues within 4Å:- Chain A: Y.160, K.166
- Chain C: R.143, F.200, R.201
Ligand excluded by PLIPEDO.19: 6 residues within 4Å:- Chain C: I.68, E.69, G.72
- Chain D: I.68, E.69, G.72
Ligand excluded by PLIPEDO.20: 6 residues within 4Å:- Chain C: P.128, F.131, L.307
- Chain D: P.128, F.131, L.307
Ligand excluded by PLIPEDO.23: 7 residues within 4Å:- Chain C: N.86, R.87, Y.88
- Chain D: K.393, A.402, L.403
- Ligands: FFO.22
Ligand excluded by PLIPEDO.24: 7 residues within 4Å:- Chain C: K.393, A.402, L.403
- Chain D: N.86, R.87, Y.88
- Ligands: FFO.17
Ligand excluded by PLIPEDO.25: 5 residues within 4Å:- Chain B: Y.160, K.166
- Chain D: R.143, F.200, R.201
Ligand excluded by PLIPEDO.26: 4 residues within 4Å:- Chain D: G.419, V.421, D.424, F.477
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Korasick, D.A. et al., Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance. Febs J. (2024)
- Release Date
- 2023-10-18
- Peptides
- Serine hydroxymethyltransferase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.63 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)
- 4 x FFO: N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid(Non-covalent)
- 18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Korasick, D.A. et al., Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance. Febs J. (2024)
- Release Date
- 2023-10-18
- Peptides
- Serine hydroxymethyltransferase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D