Research workbench
Crystal structure of human thymidylate synthase mutant Y202C
Analyse Crystal structure of human thymidylate synthase mutant Y202C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O1U
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- SO4, CL
- Pockets
- 10 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 262 | 33% helix, 25% strand | P04818 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 259 | 33% helix, 25% strand | P04818 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.60 | 0.77 | 39 | SO4, CL |
| 2 | 380 | 0.59 | 0.76 | 39 | SO4, EDO |
| 3 | 267 | 0.58 | 0.77 | 30 | EDO |
| 4 | 69 | 0.38 | 0.79 | 17 | empty |
| 5 | 94 | 0.37 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2046 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (methylation, artifact).
Compared structures
- 4O1U · Crystal structure of human thymidylate synthase mutant Y202C · 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 P04818
- Elsewhere: RCSB PDB 4O1U · PDBe 4O1U · UniProt P04818
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