- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.32 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 4 residues within 4Å:- Chain A: D.20, K.256
- Ligands: PPK.1, K.5
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.20, H2O.3, H2O.4
MG.3: 3 residues within 4Å:- Chain A: K.256
- Chain B: D.282
- Ligands: PPK.1
No protein-ligand interaction detected (PLIP)MG.4: 3 residues within 4Å:- Chain A: D.282
- Chain B: K.256
- Ligands: PPK.11
No protein-ligand interaction detected (PLIP)MG.14: 4 residues within 4Å:- Chain B: D.20, K.256
- Ligands: PPK.11, K.16
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.20, H2O.26, H2O.26
- 2 x K: POTASSIUM ION(Non-covalent)
K.5: 5 residues within 4Å:- Chain A: D.249, A.250
- Chain B: E.46
- Ligands: PPK.1, MG.2
4 PLIP interactions:2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: A:D.249, A:A.250, B:E.46, H2O.28
K.16: 5 residues within 4Å:- Chain A: E.46
- Chain B: D.249, A.250
- Ligands: PPK.11, MG.14
4 PLIP interactions:2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: B:D.249, B:A.250, A:E.46, H2O.5
- 2 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)
MPO.6: 9 residues within 4Å:- Chain A: D.40, K.42, H.111, F.114, T.115, K.116, R.117, I.121, K.358
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:H.111
- Water bridges: A:K.358, A:K.358
- Salt bridges: A:K.42, A:K.358
MPO.17: 9 residues within 4Å:- Chain B: D.40, K.42, H.111, F.114, T.115, K.116, R.117, I.121, K.358
5 PLIP interactions:5 interactions with chain B- Water bridges: B:K.358, B:K.358, B:K.358
- Salt bridges: B:K.42, B:K.358
- 1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.8: 4 residues within 4Å:- Chain A: K.94, L.96
- Chain B: V.97, N.98
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Water bridges: B:N.98
- Hydrogen bonds: A:K.94
PGE.18: 2 residues within 4Å:- Chain B: N.161, R.165
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.165
- Water bridges: B:N.161, B:R.165
- 2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)
SAM.9: 19 residues within 4Å:- Chain A: H.18, P.19, D.170, K.172, S.238, R.240, F.241, I.243, D.249
- Chain B: A.44, E.59, Q.102, D.105, I.106, G.124, D.125, K.280, I.313
- Ligands: PPK.1
18 PLIP interactions:10 interactions with chain A, 8 interactions with chain B- Hydrogen bonds: A:D.170, A:S.238, A:R.240, A:D.249, B:E.59, B:E.59, B:Q.102
- Water bridges: A:S.197, A:S.238, A:A.250, B:K.280, B:K.280, B:K.280
- Salt bridges: A:D.249, B:D.125, B:K.280
- pi-Stacking: A:F.241, A:F.241
SAM.19: 19 residues within 4Å:- Chain A: A.44, E.59, Q.102, D.105, I.106, G.124, D.125, K.280, I.313
- Chain B: H.18, P.19, D.170, K.172, S.238, R.240, F.241, I.243, D.249
- Ligands: PPK.11
18 PLIP interactions:8 interactions with chain A, 10 interactions with chain B- Hydrogen bonds: A:E.59, A:Q.102, B:D.170, B:S.238, B:R.240, B:D.249
- Water bridges: A:D.125, A:K.280, A:K.280, A:K.280, B:S.197, B:S.238, B:A.250
- Salt bridges: A:D.125, A:K.280, B:D.249
- pi-Stacking: B:F.241, B:F.241
- 2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x PDO: 1,3-PROPANDIOL(Non-covalent)
- 1 x PGR: R-1,2-PROPANEDIOL(Non-covalent)
- 1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)
PE8.15: 20 residues within 4Å:- Chain A: F.7, F.9, N.181, M.186, G.264, W.265, A.267, L.306, F.322, D.324
- Chain B: F.7, F.9, N.181, M.186, G.264, W.265, A.267, R.304, L.306, D.324
11 PLIP interactions:5 interactions with chain A, 6 interactions with chain B- Hydrogen bonds: A:G.264, B:G.264
- Water bridges: A:G.266, A:R.304, A:R.304, A:D.324, B:N.181, B:G.266, B:R.304, B:R.304, B:Y.326
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Sekula, B. et al., S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. Int.J.Biol.Macromol. (2020)
- Release Date
- 2020-02-26
- Peptides
- S-adenosylmethionine synthase 2: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.32 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
- 2 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)
- 1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)
- 2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x PDO: 1,3-PROPANDIOL(Non-covalent)
- 1 x PGR: R-1,2-PROPANEDIOL(Non-covalent)
- 1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Sekula, B. et al., S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. Int.J.Biol.Macromol. (2020)
- Release Date
- 2020-02-26
- Peptides
- S-adenosylmethionine synthase 2: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B