- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 2 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)
TYD.2: 17 residues within 4Å:- Chain A: D.9, K.13, E.36, P.37, R.47, L.51, F.64, R.68, R.90, S.94, T.95, Y.98, Q.99, R.145
- Ligands: ADP.1, MG.3, MPD.8
23 PLIP interactions:23 interactions with chain A- Hydrophobic interactions: A:R.90, A:Y.98
- Hydrogen bonds: A:D.9, A:R.68, A:Q.99, A:Q.99
- Water bridges: A:K.13, A:K.13, A:R.47, A:R.47, A:R.47, A:R.47, A:R.145, A:R.145, A:E.147, A:E.147, A:E.147
- Salt bridges: A:K.13, A:R.47, A:R.90, A:R.90, A:R.145
- pi-Stacking: A:F.64
TYD.10: 17 residues within 4Å:- Chain B: D.9, K.13, E.36, P.37, R.47, L.51, F.64, R.68, R.90, S.94, T.95, Y.98, Q.99, R.145
- Ligands: ADP.9, MG.11, MPD.14
26 PLIP interactions:26 interactions with chain B- Hydrophobic interactions: B:E.36, B:R.90, B:Y.98
- Hydrogen bonds: B:R.68, B:Q.99, B:Q.99
- Water bridges: B:K.13, B:K.13, B:T.14, B:T.14, B:T.14, B:R.47, B:R.47, B:R.47, B:D.89, B:R.145, B:R.145, B:E.147, B:E.147, B:E.147
- Salt bridges: B:K.13, B:R.47, B:R.90, B:R.90, B:R.145
- pi-Stacking: B:F.64
- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 3 residues within 4Å:- Chain A: T.14
- Ligands: ADP.1, TYD.2
4 PLIP interactions:1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:T.14, H2O.1, H2O.1, H2O.2
MG.4: 2 residues within 4Å:- Chain A: E.57, K.103
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:E.57, A:K.103, H2O.3, H2O.5, H2O.6
MG.5: 2 residues within 4Å:- Chain A: I.96, N.114
No protein-ligand interaction detected (PLIP)MG.11: 3 residues within 4Å:- Chain B: T.14
- Ligands: ADP.9, TYD.10
4 PLIP interactions:1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:T.14, H2O.8, H2O.8, H2O.10
MG.12: 2 residues within 4Å:- Chain B: E.57, K.103
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.57, B:E.57, B:K.103, H2O.8, H2O.11
MG.13: 2 residues within 4Å:- Chain B: I.96, N.114
No protein-ligand interaction detected (PLIP)- 2 x CA: CALCIUM ION(Non-covalent)
CA.6: 1 residues within 4Å:- Chain A: E.142
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:E.142, A:E.142, H2O.3, H2O.4, H2O.5
CA.7: 1 residues within 4Å:- Chain A: E.180
4 PLIP interactions:1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:E.180, H2O.3, H2O.5, H2O.6
- 2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.8: 7 residues within 4Å:- Chain A: L.50, E.60, F.64, Q.99, K.103, F.151
- Ligands: TYD.2
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:K.103, A:F.151
- Hydrogen bonds: A:L.50
MPD.14: 6 residues within 4Å:- Chain B: L.50, F.64, Q.99, K.103, F.151
- Ligands: TYD.10
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:F.64, B:F.151
- Hydrogen bonds: B:L.50, B:K.103
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Biswas, A. et al., Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate. FEBS J. (2017)
- Release Date
- 2017-06-28
- Peptides
- Thymidylate kinase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 2 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 2 x CA: CALCIUM ION(Non-covalent)
- 2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Biswas, A. et al., Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate. FEBS J. (2017)
- Release Date
- 2017-06-28
- Peptides
- Thymidylate kinase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B