- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.92 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 15 x CA: CALCIUM ION(Non-covalent)
CA.2: 1 residues within 4Å:- Chain A: R.187
No protein-ligand interaction detected (PLIP)CA.3: 5 residues within 4Å:- Chain A: Q.19, R.22, L.23, A.186, I.189
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:Q.19, H2O.3
CA.4: 3 residues within 4Å:- Chain A: E.61, R.104, E.148
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.61, H2O.1
CA.5: 1 residues within 4Å:- Chain A: S.49
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:S.49
CA.6: 2 residues within 4Å:- Chain A: T.17
- Ligands: ADP.1
5 PLIP interactions:1 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:T.17, H2O.1, H2O.1, H2O.2, H2O.3
CA.7: 4 residues within 4Å:- Chain A: Y.62, S.66, R.69, L.93
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:Y.62, A:S.66
CA.8: 5 residues within 4Å:- Chain A: E.39, P.40, F.65, D.68, R.69
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:D.68
CA.9: 5 residues within 4Å:- Chain A: T.7, E.9, Y.92, D.94, T.127
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:T.7, A:E.9, A:D.94
CA.10: 5 residues within 4Å:- Chain A: G.10, L.11, L.130, D.131, L.132
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:L.130, H2O.2
CA.15: 2 residues within 4Å:- Chain B: T.17
- Ligands: ADP.14
5 PLIP interactions:1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:T.17, H2O.4, H2O.5, H2O.6, H2O.6
CA.16: 5 residues within 4Å:- Chain B: Y.62, S.66, R.69, L.93, A.115
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:S.66
CA.17: 4 residues within 4Å:- Chain B: E.160, L.163, A.164, R.167
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:E.160, B:E.160
CA.18: 3 residues within 4Å:- Chain B: P.134, E.135, A.137
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:A.137
CA.19: 4 residues within 4Å:- Chain B: Y.102, R.157, E.160, G.161
4 PLIP interactions:1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:R.157, H2O.5, H2O.6, H2O.7
CA.20: 5 residues within 4Å:- Chain B: E.39, P.40, F.65, D.68, R.69
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:F.65, B:D.68
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)
TMP.13: 12 residues within 4Å:- Chain A: D.12, E.39, P.40, R.48, F.65, R.69, R.91, S.95, S.96, Y.99, Q.100, L.150
15 PLIP interactions:15 interactions with chain A- Hydrophobic interactions: A:E.39, A:F.65, A:R.91, A:Y.99
- Hydrogen bonds: A:D.12, A:R.69, A:Q.100, A:Q.100
- Water bridges: A:K.16, A:K.16, A:K.16, A:R.91
- Salt bridges: A:R.48, A:R.91
- pi-Stacking: A:F.65
TMP.22: 11 residues within 4Å:- Chain B: D.12, E.39, P.40, R.48, F.65, R.69, R.91, S.95, S.96, Y.99, Q.100
7 PLIP interactions:7 interactions with chain B- Hydrophobic interactions: B:E.39, B:Y.99
- Hydrogen bonds: B:R.69, B:Q.100, B:Q.100
- Salt bridges: B:R.48
- pi-Stacking: B:F.65
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Chaudhary, S.K. et al., Insights into product release dynamics through structural analyses of thymidylate kinase. Int. J. Biol. Macromol. (2018)
- Release Date
- 2018-12-19
- Peptides
- Thymidylate kinase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.92 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 15 x CA: CALCIUM ION(Non-covalent)
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Chaudhary, S.K. et al., Insights into product release dynamics through structural analyses of thymidylate kinase. Int. J. Biol. Macromol. (2018)
- Release Date
- 2018-12-19
- Peptides
- Thymidylate kinase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B