MolNFT v1 · #47058 · protein
Human thymidylate synthase at low salt conditions with pdpa bound
2ONB · Thymidylate synthetase: “Human thymidylate synthase at low salt conditions with pdpa bound”. X-ray diffraction, 2 ligands (7PA, SO4), 4 pockets (best druggability 0.57). MolNFT v1 #47058 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2ONB
- Type
- protein
- Length
- 264 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthetase
- UniProt
- Q53Y97
- Ligands
- 7PA, SO4
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthetase | protein | 264 | 31% helix, 23% strand | Q53Y97 |
Ligands and binding sites
- 7PA · Propane-1,3-diylbis(phosphonic acid) · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.57 | 0.75 | 41 | 7PA |
| 2 | 61 | 0.33 | 0.76 | 13 | empty |
| 3 | 51 | 0.30 | 0.75 | 13 | empty |
| 4 | 57 | 0.26 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- 2ONB · Human Thymidylate Synthase at low salt conditions with PDPA bound · the same entry in another collection · chain A against A, TM-score 1.00
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 Q53Y97
- Elsewhere: RCSB PDB 2ONB · PDBe 2ONB · UniProt Q53Y97
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