MolNFT v1 · #139289 · protein
ADP-dtmp bound crystal structure of thymidylate kinase (AQ_969) from aquifex aeolicus VF5
5XB3: “ADP-dtmp bound crystal structure of thymidylate kinase (AQ_969) from aquifex aeolicus VF5”. X-ray diffraction, 2 ligands (ADP, TMP), 4 pockets (best druggability 0.62). MolNFT v1 #139289 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XB3
- Type
- protein
- Length
- 387 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
- ADP, TMP
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 193 | 59% helix, 13% strand | O67099 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 194 | 58% helix, 13% strand | O67099 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- TMP · Thymidine-5'-phosphate · ligand · 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 | 324 | 0.62 | 0.79 | 39 | ADP, TMP |
| 2 | 325 | 0.61 | 0.78 | 40 | ADP, TMP |
| 3 | 120 | 0.50 | 0.80 | 18 | empty |
| 4 | 119 | 0.48 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1152 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5XB3 · ADP-dTMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5 · the same entry in another collection · chain B against B, TM-score 1.00
- O67099 · AlphaFold monomer V2.0 prediction for thymidylate kinase (O67099) · a predicted model of the same protein · chain B 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 5XB3 · PDBe 5XB3 · UniProt O67099
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.