Research workbench
Thymidylate synthase from rat in ternary complex with dump and tomudex
Analyse Thymidylate synthase from rat in ternary complex with dump and tomudex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RTS
- Type
- protein
- Length
- 563 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P45352
- Ligands
- UMP, D16
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 280 | 33% helix, 24% strand | P45352 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 283 | 33% helix, 23% strand | P45352 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- D16 · Tomudex · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.69 | 0.80 | 54 | UMP, D16 |
| 2 | 362 | 0.67 | 0.81 | 47 | UMP, D16 |
| 3 | 155 | 0.49 | 0.77 | 19 | empty |
| 4 | 132 | 0.47 | 0.77 | 16 | empty |
| 5 | 73 | 0.41 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2190 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1RTS · Thymidylate synthase from rat in ternary complex with dump and tomudex · the same entry in another collection · chain A against A, TM-score 1.00
- P45352 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P45352) · a predicted model of the same protein · chain B 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 P45352
- Elsewhere: RCSB PDB 1RTS · PDBe 1RTS · UniProt P45352
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