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
- 2TSR
- Type
- protein
- Length
- 1,124 residues
- Chains
- 4
- 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
- 20 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 35% helix, 23% strand | P45352 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- D16 · Tomudex · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.70 | 0.79 | 57 | UMP, D16 |
| 2 | 491 | 0.68 | 0.79 | 46 | UMP, D16 |
| 3 | 447 | 0.67 | 0.79 | 42 | UMP, D16 |
| 4 | 421 | 0.66 | 0.79 | 41 | UMP, D16 |
| 5 | 229 | 0.58 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2279 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2216 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 674 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2TSR · Thymidylate synthase from rat in ternary complex with dump and tomudex · the same entry in another collection · chain B against B, 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 2TSR · PDBe 2TSR · UniProt P45352
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