MolNFT v1 · #89466 · protein
Thymidylate synthase from staphylococcus aureus.
4DQ1: “Thymidylate synthase from staphylococcus aureus.”. X-ray diffraction, 1 ligand (UMP), 9 pockets (best druggability 0.68). MolNFT v1 #89466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DQ1
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P67046
- Ligands
- UMP
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 312 | 41% helix, 22% strand | P67046 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 300 | 39% helix, 23% strand | P67046 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.68 | 0.80 | 39 | UMP |
| 2 | 542 | 0.68 | 0.78 | 50 | UMP |
| 3 | 50 | 0.51 | 0.88 | 20 | empty |
| 4 | 84 | 0.47 | 0.82 | 13 | empty |
| 5 | 96 | 0.45 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2478 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
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 P67046
- Elsewhere: RCSB PDB 4DQ1 · PDBe 4DQ1 · UniProt P67046
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