MolNFT v1 · #139288 · protein
ADP-mg-F-dtmp bound crystal structure of thymidylate kinase (AQ_969) from aquifex aeolicus VF5
5XB2: “ADP-mg-F-dtmp bound crystal structure of thymidylate kinase (AQ_969) from aquifex aeolicus VF5”. X-ray diffraction, 4 ligands (ADP, TMP, MG), 3 pockets (best druggability 0.63). MolNFT v1 #139288 on GenesisL1: 3D structure, binding…
- PDB
- 5XB2
- Type
- protein
- Length
- 388 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, MG, F
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | 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 B, A
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · chains B
- F · Fluoride ion · ion · 3 copies · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.63 | 0.79 | 44 | ADP, TMP |
| 2 | 315 | 0.61 | 0.79 | 39 | ADP, TMP, MG, F |
| 3 | 97 | 0.44 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- B–A · 1127 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5XB2 · ADP-Mg-F-dTMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex… · 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 5XB2 · PDBe 5XB2 · UniProt O67099
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