MolNFT v1 · #93118 · protein
Crystal structure of thymidylate kinase from staphylococcus aureus bound to inhibitor.
4GSY: “Crystal structure of thymidylate kinase from staphylococcus aureus bound to inhibitor.”. X-ray diffraction, 1 ligand (0Y5), 2 pockets (best druggability 0.54). MolNFT v1 #93118 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4GSY
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- P65249
- Ligands
- 0Y5
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 191 | 59% helix, 14% strand | P65249 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 193 | 61% helix, 14% strand | P65249 |
Ligands and binding sites
- 0Y5 · 4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}-2-[3-(trifluoromethyl)phenoxy]benzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.54 | 0.79 | 22 | 0Y5 |
| 2 | 184 | 0.50 | 0.77 | 22 | 0Y5 |
Interfaces
1 interface between chains.
- A–B · 1080 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4GSY · Crystal structure of thymidylate kinase from Staphylococcus aureus bound to inhibitor. · the same entry in another collection · chain A against A, TM-score 1.00
- P65249 · AlphaFold monomer V2.0 prediction for thymidylate kinase (P65249) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P65249
- Elsewhere: RCSB PDB 4GSY · PDBe 4GSY · UniProt P65249
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.