- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.39 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x POP: PYROPHOSPHATE 2-(Non-covalent)
- 8 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.2: 11 residues within 4Å:- Chain A: D.25, R.253, K.254
- Chain B: G.268, G.269, A.270, K.274, D.280
- Ligands: POP.1, MG.6, MG.12
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain B- Salt bridges: A:R.253, A:K.254, B:K.274
- Hydrogen bonds: B:A.270
PO4.3: 11 residues within 4Å:- Chain A: G.268, G.269, A.270, K.274, D.280
- Chain B: D.25, R.253, K.254
- Ligands: MG.7, POP.11, MG.13
4 PLIP interactions:2 interactions with chain B, 2 interactions with chain A- Salt bridges: B:R.253, B:K.254, A:K.274
- Hydrogen bonds: A:A.270
PO4.4: 5 residues within 4Å:- Chain A: H.23, D.172, K.174, F.239
- Ligands: POP.1
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Salt bridges: A:H.23, A:K.174
- Water bridges: B:D.127
PO4.5: 3 residues within 4Å:- Chain A: E.315, D.343
- Chain B: R.5
5 PLIP interactions:4 interactions with chain A, 1 interactions with chain B- Water bridges: A:R.339, A:F.342, A:L.344
- Salt bridges: A:R.345, B:R.5
PO4.18: 11 residues within 4Å:- Chain C: D.25, R.253, K.254
- Chain D: G.268, G.269, A.270, K.274, D.280
- Ligands: POP.17, MG.22, MG.28
4 PLIP interactions:2 interactions with chain D, 2 interactions with chain C- Hydrogen bonds: D:A.270
- Salt bridges: D:K.274, C:R.253, C:K.254
PO4.19: 11 residues within 4Å:- Chain C: G.268, G.269, A.270, K.274, D.280
- Chain D: D.25, R.253, K.254
- Ligands: MG.23, POP.27, MG.29
4 PLIP interactions:2 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:A.270
- Salt bridges: C:K.274, D:R.253, D:K.254
PO4.20: 5 residues within 4Å:- Chain C: H.23, D.172, K.174, F.239
- Ligands: POP.17
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain D- Salt bridges: C:H.23, C:K.174
- Water bridges: D:D.127
PO4.21: 3 residues within 4Å:- Chain C: E.315, D.343
- Chain D: R.5
5 PLIP interactions:1 interactions with chain D, 4 interactions with chain C- Salt bridges: D:R.5, C:R.345
- Water bridges: C:R.339, C:F.342, C:L.344
- 8 x MG: MAGNESIUM ION(Non-covalent)
MG.6: 5 residues within 4Å:- Chain A: D.25, D.247, K.254
- Ligands: POP.1, PO4.2
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.25, H2O.1, H2O.2
MG.7: 3 residues within 4Å:- Chain A: D.280
- Ligands: PO4.3, POP.11
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:D.280
MG.12: 3 residues within 4Å:- Chain B: D.280
- Ligands: POP.1, PO4.2
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:D.280
MG.13: 4 residues within 4Å:- Chain B: D.25, K.254
- Ligands: PO4.3, POP.11
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.25, H2O.4, H2O.5
MG.22: 5 residues within 4Å:- Chain C: D.25, D.247, K.254
- Ligands: POP.17, PO4.18
3 PLIP interactions:1 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.25, H2O.6, H2O.7
MG.23: 3 residues within 4Å:- Chain C: D.280
- Ligands: PO4.19, POP.27
1 PLIP interactions:1 interactions with chain C- Metal complexes: C:D.280
MG.28: 3 residues within 4Å:- Chain D: D.280
- Ligands: POP.17, PO4.18
1 PLIP interactions:1 interactions with chain D- Metal complexes: D:D.280
MG.29: 4 residues within 4Å:- Chain D: D.25, K.254
- Ligands: PO4.19, POP.27
3 PLIP interactions:1 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.25, H2O.9, H2O.10
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.8: 2 residues within 4Å:- Chain A: K.217, F.231
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.217
EDO.9: 4 residues within 4Å:- Chain A: K.217, P.218, I.219, P.221
No protein-ligand interaction detected (PLIP)EDO.10: 4 residues within 4Å:- Chain A: D.127
- Chain B: H.23, D.172
- Ligands: POP.11
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:D.127, B:D.172
EDO.14: 2 residues within 4Å:- Chain B: E.41, Q.42
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Q.42
EDO.15: 6 residues within 4Å:- Chain B: S.89, D.90
- Chain D: V.87, H.88, D.94, N.96
4 PLIP interactions:2 interactions with chain B, 2 interactions with chain D- Hydrogen bonds: B:D.90, B:D.90, D:D.94, D:N.96
EDO.16: 6 residues within 4Å:- Chain B: Y.289, M.352, D.354, P.375, K.378, D.380
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:D.380
EDO.24: 2 residues within 4Å:- Chain C: K.217, F.231
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:K.217
EDO.25: 4 residues within 4Å:- Chain C: K.217, P.218, I.219, P.221
No protein-ligand interaction detected (PLIP)EDO.26: 4 residues within 4Å:- Chain C: D.127
- Chain D: H.23, D.172
- Ligands: POP.27
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:D.127, D:D.172
EDO.30: 2 residues within 4Å:- Chain D: E.41, Q.42
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:Q.42
EDO.31: 6 residues within 4Å:- Chain B: V.87, H.88, D.94, N.96
- Chain D: S.89, D.90
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:D.94, B:N.96, D:D.90
EDO.32: 6 residues within 4Å:- Chain D: Y.289, M.352, D.354, P.375, K.378, D.380
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:Y.289, D:D.380
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gade, M. et al., Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. Jacs Au (2021)
- Release Date
- 2021-03-31
- Peptides
- S-adenosylmethionine synthase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.39 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x POP: PYROPHOSPHATE 2-(Non-covalent)
- 8 x PO4: PHOSPHATE ION(Non-functional Binders)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gade, M. et al., Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. Jacs Au (2021)
- Release Date
- 2021-03-31
- Peptides
- S-adenosylmethionine synthase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B