Research workbench
Crystal structure of the thymidylate synthase K48Q complexed with 5NO2DUMP and BW1843U89
Analyse Crystal structure of the thymidylate synthase K48Q complexed with 5NO2DUMP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VF0
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P0A884
- Ligands
- NDU, F89, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 34% helix, 26% strand | P0A884 |
Ligands and binding sites
- NDU · 2'-deoxy-5-nitrouridine 5'-monophosphate · ligand · 2 copies · chains A, B
- F89 · S)-2-(5(((1,2-dihydro-3-methyl-1-oxobenzo(f)quinazolin-9-yl)methyl)amino)1-oxo-2-isoindolinyl)glutaric acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.77 | 0.85 | 51 | NDU, F89 |
| 2 | 515 | 0.77 | 0.84 | 46 | NDU, F89 |
| 3 | 115 | 0.43 | 0.77 | 18 | empty |
| 4 | 104 | 0.41 | 0.77 | 18 | empty |
| 5 | 90 | 0.41 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2335 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 2VF0 · Crystal structure of the thymidylate synthase K48Q complexed with 5NO2DUMP and BW1843U89 · the same entry in another collection · chain A against A, TM-score 1.00
- P0A884 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P0A884) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0A884
- Elsewhere: RCSB PDB 2VF0 · PDBe 2VF0 · UniProt P0A884
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