- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x K: POTASSIUM ION(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 3 residues within 4Å:- Chain A: E.8, K.165
- Ligands: PPK.5
No protein-ligand interaction detected (PLIP)MG.3: 3 residues within 4Å:- Chain A: D.16, K.245
- Ligands: PPK.5
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:D.16
MG.7: 3 residues within 4Å:- Chain B: E.8, K.165
- Ligands: PPK.10
No protein-ligand interaction detected (PLIP)MG.8: 4 residues within 4Å:- Chain B: D.16, R.244, K.245
- Ligands: PPK.10
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:D.16, B:D.16
MG.12: 4 residues within 4Å:- Chain C: D.16, C.239
- Ligands: K.11, PPK.16
2 PLIP interactions:2 interactions with chain C- Metal complexes: C:D.16, C:D.16
MG.13: 5 residues within 4Å:- Chain C: D.118, Q.119, D.271
- Chain D: K.165
- Ligands: PPK.20
No protein-ligand interaction detected (PLIP)MG.17: 5 residues within 4Å:- Chain C: K.165
- Chain D: D.118, Q.119, D.271
- Ligands: PPK.16
No protein-ligand interaction detected (PLIP)MG.19: 3 residues within 4Å:- Chain D: D.16, K.245
- Ligands: PPK.20
2 PLIP interactions:2 interactions with chain D- Metal complexes: D:D.16, D:D.16
- 4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)
SAM.4: 19 residues within 4Å:- Chain A: H.14, P.15, D.163, K.165, S.186, T.227, R.229, F.230, D.238
- Chain B: A.40, E.55, Q.98, D.101, I.102, G.117, D.118, K.269, I.302
- Ligands: PPK.5
15 PLIP interactions:11 interactions with chain A, 4 interactions with chain B- Hydrogen bonds: A:D.163, A:S.186, A:T.227, A:D.238, A:D.238, A:D.238, B:E.55, B:Q.98
- Water bridges: A:R.229, A:G.237
- Salt bridges: A:D.238, B:D.118, B:K.269
- pi-Stacking: A:F.230, A:F.230
SAM.9: 19 residues within 4Å:- Chain A: A.40, E.55, Q.98, D.101, I.102, G.117, D.118, K.269, I.302
- Chain B: H.14, P.15, D.163, K.165, S.186, T.227, R.229, F.230, D.238
- Ligands: PPK.10
12 PLIP interactions:8 interactions with chain B, 4 interactions with chain A- Hydrogen bonds: B:D.163, B:S.186, B:T.227, B:T.227, B:D.238, A:E.55, A:Q.98
- Salt bridges: B:D.238, A:D.118, A:K.269
- pi-Stacking: B:F.230, B:F.230
SAM.14: 20 residues within 4Å:- Chain C: H.14, P.15, D.163, K.165, S.186, T.227, R.229, F.230, I.232, D.238
- Chain D: A.40, E.55, Q.98, D.101, I.102, G.117, D.118, K.269, I.302
- Ligands: PPK.16
18 PLIP interactions:8 interactions with chain D, 10 interactions with chain C- Hydrogen bonds: D:E.55, D:Q.98, C:D.163, C:S.186, C:T.227, C:T.227, C:D.238
- Water bridges: D:D.101, D:I.102, D:K.269, D:K.269, C:T.227, C:R.229
- Salt bridges: D:D.118, D:K.269, C:D.238
- pi-Stacking: C:F.230, C:F.230
SAM.15: 21 residues within 4Å:- Chain C: A.40, E.55, Q.98, D.101, I.102, G.117, D.118, K.269, I.302
- Chain D: H.14, P.15, D.163, K.165, S.186, T.227, R.229, F.230, I.232, G.237, D.238
- Ligands: PPK.20
17 PLIP interactions:11 interactions with chain D, 6 interactions with chain C- Hydrogen bonds: D:D.163, D:S.186, D:T.227, D:D.238, D:D.238, D:D.238, C:E.55, C:Q.98
- Water bridges: D:T.227, D:I.232, C:I.102, C:K.269
- Salt bridges: D:D.238, C:D.118, C:K.269
- pi-Stacking: D:F.230, D:F.230
- 4 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)
PPK.5: 16 residues within 4Å:- Chain A: H.14, D.16, K.165, D.238, R.244, K.245
- Chain B: D.118, G.259, G.260, A.261, K.265, D.271
- Ligands: K.1, MG.2, MG.3, SAM.4
11 PLIP interactions:6 interactions with chain B, 5 interactions with chain A- Hydrogen bonds: B:D.118, B:A.261, B:K.265, B:K.265, B:K.265, B:D.271, A:R.244, A:K.245
- Salt bridges: A:H.14, A:K.165, A:K.245
PPK.10: 16 residues within 4Å:- Chain A: D.118, G.259, G.260, A.261, K.265, D.271
- Chain B: H.14, D.16, K.165, D.238, R.244, K.245
- Ligands: K.6, MG.7, MG.8, SAM.9
10 PLIP interactions:5 interactions with chain A, 5 interactions with chain B- Hydrogen bonds: A:E.42, A:A.261, A:K.265, A:K.265, A:K.265, B:R.244, B:K.245
- Salt bridges: B:H.14, B:K.165, B:K.245
PPK.16: 17 residues within 4Å:- Chain C: H.14, D.16, K.165, D.238, R.244, K.245
- Chain D: E.42, D.118, G.259, G.260, A.261, K.265, D.271
- Ligands: K.11, MG.12, SAM.14, MG.17
12 PLIP interactions:7 interactions with chain C, 5 interactions with chain D- Hydrogen bonds: C:D.16, C:R.244, C:R.244, C:K.245, D:E.42, D:A.261, D:K.265, D:K.265, D:K.265
- Salt bridges: C:H.14, C:K.165, C:K.245
PPK.20: 16 residues within 4Å:- Chain C: D.118, G.259, G.260, A.261, K.265, D.271
- Chain D: H.14, D.16, K.165, D.238, R.244, K.245
- Ligands: MG.13, SAM.15, K.18, MG.19
12 PLIP interactions:6 interactions with chain D, 6 interactions with chain C- Hydrogen bonds: D:R.244, D:R.244, D:K.245, C:D.118, C:G.259, C:A.261, C:K.265, C:K.265, C:K.265
- Salt bridges: D:H.14, D:K.165, D:K.245
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Komoto, J. et al., Crystal structure of the S-adenosylmethionine synthetase ternary complex: a novel catalytic mechanism of s-adenosylmethionine synthesis from ATP and MET. Biochemistry (2004)
- Release Date
- 2004-03-02
- Peptides
- S-adenosylmethionine synthetase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x K: POTASSIUM ION(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)
- 4 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Komoto, J. et al., Crystal structure of the S-adenosylmethionine synthetase ternary complex: a novel catalytic mechanism of s-adenosylmethionine synthesis from ATP and MET. Biochemistry (2004)
- Release Date
- 2004-03-02
- Peptides
- S-adenosylmethionine synthetase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D