MolNFT v1 · #106542 · protein
Phosphate ion bound crystal structure of thymidylate kinase (AQ_969) from aquifex aeolicus VF5
4S2E: “Phosphate ion bound crystal structure of thymidylate kinase (AQ_969) from aquifex aeolicus VF5”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.58). MolNFT v1 #106542 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4S2E
- Type
- protein
- Length
- 383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- O67099
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 190 | 59% helix, 14% strand | O67099 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 193 | 59% helix, 13% strand | O67099 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.58 | 0.81 | 23 | empty |
| 2 | 213 | 0.57 | 0.79 | 26 | empty |
| 3 | 103 | 0.50 | 0.81 | 20 | empty |
| 4 | 131 | 0.49 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1098 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4S2E · Phosphate ion bound Crystal structure of thymidylate kinase (aq_969) from Aquifex… · the same entry in another collection · chain A against A, TM-score 1.00
- O67099 · AlphaFold monomer V2.0 prediction for thymidylate kinase (O67099) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O67099
- Elsewhere: RCSB PDB 4S2E · PDBe 4S2E · UniProt O67099
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