Research workbench
Thymidylate synthase complex with 2'-deoxyuridine 5'-monophosphate (dump) and folate analog 1843U89
Analyse Thymidylate synthase complex with 2'-deoxyuridine 5'-monophosphate (dump) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TSD
- 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
- P00470
- Ligands
- UMP, F89
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 36% helix, 26% strand | P00470 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 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
- FMT · Formic acid · additive · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.77 | 0.85 | 46 | BME, UMP, F89 |
| 2 | 415 | 0.77 | 0.86 | 40 | UMP, F89 |
| 3 | 114 | 0.41 | 0.76 | 19 | empty |
| 4 | 104 | 0.41 | 0.77 | 18 | empty |
| 5 | 97 | 0.40 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2361 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 1TSD · Thymidylate synthase complex with 2'-deoxyuridine 5'-monophosphate (dump) and folate… · 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 P00470
- Elsewhere: RCSB PDB 1TSD · PDBe 1TSD · UniProt P00470
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.