Research workbench
Human thymidylate synthase with a fragment bound in the dimer interface
Analyse Human thymidylate synthase with a fragment bound in the dimer interface in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X69
- Type
- protein
- Length
- 1,692 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.69
- Source
- Homo sapiens
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- UMP, 7ZC
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.69 · 6 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 287 | 34% helix, 23% strand | P04818 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 34% helix, 23% strand | P04818 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 277 | 35% helix, 24% strand | P04818 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 285 | 34% helix, 23% strand | P04818 |
| E | Thymidylate synthase (EC 2.1.1.45) | protein | 276 | 35% helix, 24% strand | P04818 |
| F | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 35% helix, 23% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, D, B, E, C, F
- 7ZC · 1-(5-methoxy-1H-indol-3-yl)-N,N-dimethyl-methanamine · ligand · 2 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.79 | 0.82 | 83 | UMP |
| 2 | 477 | 0.74 | 0.83 | 44 | UMP |
| 3 | 1079 | 0.74 | 0.77 | 78 | empty |
| 4 | 512 | 0.69 | 0.79 | 52 | UMP |
| 5 | 395 | 0.64 | 0.78 | 34 | UMP |
Interfaces
6 interfaces between chains.
- A–D · 2243 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 2170 Ų buried · 28 hydrogen bonds · protein-protein
- B–E · 2122 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 403 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 293 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5X69 · Human thymidylate synthase with a fragment bound in the dimer interface · the same entry in another collection · chain F against F, TM-score 1.00
- P04818 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P04818) · 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 P04818
- Elsewhere: RCSB PDB 5X69 · PDBe 5X69 · UniProt P04818
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