Research workbench
Crystal structure of thymidylate kinase in complex with ADP and tmp from thermus thermophilus HB8
Analyse Crystal structure of thymidylate kinase in complex with ADP and tmp from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZB4
- Type
- protein
- Length
- 371 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q5SHX3
- Ligands
- ADP, TMP, CA, CL
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 186 | 52% helix, 15% strand | Q5SHX3 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 185 | 55% helix, 15% strand | Q5SHX3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 15 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.56 | 0.80 | 32 | CA, TMP |
| 2 | 181 | 0.50 | 0.77 | 24 | TMP |
| 3 | 54 | 0.38 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1057 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5ZB4 · Crystal structure of thymidylate kinase in complex with ADP and TMP from thermus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SHX3 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q5SHX3) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q5SHX3
- Elsewhere: RCSB PDB 5ZB4 · PDBe 5ZB4 · UniProt Q5SHX3
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