- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.34 Å
- Oligo State
- homo-dimer
- Ligands
- 1 x MDN: METHYLENEDIPHOSPHONIC ACID(Non-covalent)
- 5 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 7 residues within 4Å:- Chain A: K.26, H.30, D.32, R.286
- Ligands: MDN.1, PO4.4, MG.6
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.32, H2O.1, H2O.1
MG.5: 8 residues within 4Å:- Chain A: K.26
- Chain B: D.159, S.161, E.303, K.308, H.313
- Ligands: MDN.1, PO4.4
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:E.303, B:E.303, H2O.3
MG.6: 8 residues within 4Å:- Chain A: D.280, D.281, R.286
- Chain B: D.63, Q.64
- Ligands: MDN.1, MG.2, SAM.3
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.63, H2O.1, H2O.5
MG.9: 6 residues within 4Å:- Chain B: K.26, H.30, D.32, R.286
- Ligands: ACP.7, PO4.8
4 PLIP interactions:1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:D.32, H2O.3, H2O.4, H2O.4
MG.10: 5 residues within 4Å:- Chain B: E.24, K.26, K.200
- Ligands: ACP.7, PO4.8
No protein-ligand interaction detected (PLIP)- 1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)
SAM.3: 24 residues within 4Å:- Chain A: H.30, P.31, D.198, K.200, A.215, N.257, T.258, A.259, Y.268, S.275, G.279, D.280, D.281
- Chain B: H.59, N.61, R.92, D.141, L.142, N.158, D.159, H.313, I.346
- Ligands: MDN.1, MG.6
20 PLIP interactions:12 interactions with chain A, 8 interactions with chain B- Hydrogen bonds: A:D.198, A:K.200, A:Y.268, A:S.275, A:D.280, A:D.280, B:N.61, B:D.141, B:D.141, B:N.158
- Water bridges: A:D.198, A:Y.268, A:D.281
- Salt bridges: A:D.280, B:H.59, B:D.159, B:H.313
- pi-Stacking: A:Y.268, A:Y.268
- Hydrophobic interactions: B:L.142
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.4: 11 residues within 4Å:- Chain A: K.26, D.32, R.286
- Chain B: D.63, M.302, E.303, A.304, K.308
- Ligands: MDN.1, MG.2, MG.5
7 PLIP interactions:4 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:D.63, B:D.63, B:A.304
- Salt bridges: B:K.308, A:K.26, A:R.286
- Water bridges: A:K.26
PO4.8: 10 residues within 4Å:- Chain A: M.302, E.303, A.304, K.308
- Chain B: K.26, D.32, R.286
- Ligands: ACP.7, MG.9, MG.10
13 PLIP interactions:9 interactions with chain B, 4 interactions with chain A- Hydrogen bonds: B:R.286, A:D.63, A:D.63, A:A.304
- Water bridges: B:K.26, B:K.26, B:K.26, B:R.286, B:R.286, B:R.286
- Salt bridges: B:K.26, B:R.286, A:K.308
- 1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)
ACP.7: 17 residues within 4Å:- Chain A: K.308, H.313
- Chain B: K.26, H.30, P.31, D.32, D.198, K.200, A.215, N.257, A.259, Y.268, S.275, D.280
- Ligands: PO4.8, MG.9, MG.10
12 PLIP interactions:11 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:K.26, B:H.30, B:D.198, B:D.198, B:K.200, B:Y.268, A:H.313
- Water bridges: B:A.259, B:D.260
- Salt bridges: B:K.200
- pi-Stacking: B:Y.268, B:Y.268
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Minici, C. et al., Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues. J.Struct.Biol. (2020)
- Release Date
- 2020-02-05
- Peptides
- S-adenosylmethionine synthase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EB
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.34 Å
- Oligo State
- homo-dimer
- Ligands
- 1 x MDN: METHYLENEDIPHOSPHONIC ACID(Non-covalent)
- 5 x MG: MAGNESIUM ION(Non-covalent)
- 1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Minici, C. et al., Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues. J.Struct.Biol. (2020)
- Release Date
- 2020-02-05
- Peptides
- S-adenosylmethionine synthase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EB
F