- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.25 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.5, MG.11
6 PLIP interactions:4 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:A.270, B:D.280, B:D.280
- Salt bridges: B:K.274, A:R.253, A:K.254
PO4.3: 6 residues within 4Å:- Chain A: H.23, D.172, K.174, F.239
- Chain B: D.127
- Ligands: POP.1
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:D.172
- Salt bridges: A:K.174
- Water bridges: B:D.127
PO4.4: 4 residues within 4Å:- Chain A: E.315, D.343, R.345
- Chain B: R.5
4 PLIP interactions:1 interactions with chain B, 3 interactions with chain A- Salt bridges: B:R.5, A:R.345
- Water bridges: A:R.339, A:L.344
PO4.10: 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.6, POP.9, MG.12
5 PLIP interactions:3 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:A.270, A:A.270
- Salt bridges: A:K.274, B:R.253, B:K.254
PO4.17: 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.16, MG.20, MG.26
5 PLIP interactions:2 interactions with chain C, 3 interactions with chain D- Salt bridges: C:R.253, C:K.254, D:K.274
- Hydrogen bonds: D:A.270, D:D.280
PO4.18: 6 residues within 4Å:- Chain C: H.23, D.172, K.174, F.239
- Chain D: D.127
- Ligands: POP.16
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain C- Water bridges: D:D.127
- Hydrogen bonds: C:D.172
- Salt bridges: C:K.174
PO4.19: 4 residues within 4Å:- Chain C: E.315, D.343, R.345
- Chain D: R.5
4 PLIP interactions:1 interactions with chain D, 3 interactions with chain C- Salt bridges: D:R.5, C:R.345
- Water bridges: C:R.339, C:L.344
PO4.25: 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.21, POP.24, MG.27
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:A.270, C:A.270, C:D.280
- Salt bridges: C:K.274, D:R.253, D:K.254
- 8 x MG: MAGNESIUM ION(Non-covalent)
MG.5: 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.6: 3 residues within 4Å:- Chain A: D.280
- Ligands: POP.9, PO4.10
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.280, H2O.5
MG.11: 3 residues within 4Å:- Chain B: D.280
- Ligands: POP.1, PO4.2
4 PLIP interactions:1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:D.280, H2O.1, H2O.2, H2O.4
MG.12: 4 residues within 4Å:- Chain B: D.25, K.254
- Ligands: POP.9, PO4.10
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.25, H2O.5, H2O.5
MG.20: 5 residues within 4Å:- Chain C: D.25, D.247, K.254
- Ligands: POP.16, PO4.17
3 PLIP interactions:1 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.25, H2O.7, H2O.8
MG.21: 3 residues within 4Å:- Chain C: D.280
- Ligands: POP.24, PO4.25
2 PLIP interactions:1 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.280, H2O.11
MG.26: 3 residues within 4Å:- Chain D: D.280
- Ligands: POP.16, PO4.17
4 PLIP interactions:1 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:D.280, H2O.7, H2O.8, H2O.10
MG.27: 4 residues within 4Å:- Chain D: D.25, K.254
- Ligands: POP.24, PO4.25
3 PLIP interactions:1 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.25, H2O.11, H2O.11
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 3 residues within 4Å:- Chain A: K.217, L.225, T.226
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:L.225
EDO.8: 5 residues within 4Å:- Chain A: K.217, P.218, I.219, L.220, P.221
No protein-ligand interaction detected (PLIP)EDO.13: 1 residues within 4Å:- Chain B: Q.42
No protein-ligand interaction detected (PLIP)EDO.14: 6 residues within 4Å:- Chain B: S.89, D.90
- Chain D: V.87, H.88, D.94, N.96
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain B- Hydrogen bonds: D:V.87, B:D.90
EDO.15: 5 residues within 4Å:- Chain B: Y.289, M.352, L.353, P.375, D.380
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:D.380
EDO.22: 3 residues within 4Å:- Chain C: K.217, L.225, T.226
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:L.225
EDO.23: 5 residues within 4Å:- Chain C: K.217, P.218, I.219, L.220, P.221
No protein-ligand interaction detected (PLIP)EDO.28: 1 residues within 4Å:- Chain D: Q.42
No protein-ligand interaction detected (PLIP)EDO.29: 6 residues within 4Å:- Chain B: V.87, H.88, D.94, N.96
- Chain D: S.89, D.90
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:V.87
EDO.30: 5 residues within 4Å:- Chain D: Y.289, M.352, L.353, P.375, 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 2.25 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)
- 10 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