MolNFT v1 · #101790 · protein
Crystal structure of human thymidylate synthase double mutant C195S- Y202C
4O1X: “Crystal structure of human thymidylate synthase double mutant C195S- Y202C”. X-ray diffraction, 2 ligands (SO4, CL), 19 pockets (best druggability 0.73). MolNFT v1 #101790 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4O1X
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- 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
- 19 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 288 | 33% helix, 23% strand | P04818 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 35% helix, 23% strand | P04818 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 278 | 35% helix, 24% strand | P04818 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, D
- CL · Chloride ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.73 | 0.80 | 64 | SO4 |
| 2 | 687 | 0.72 | 0.79 | 58 | CL, SO4 |
| 3 | 556 | 0.67 | 0.77 | 52 | SO4 |
| 4 | 420 | 0.65 | 0.78 | 37 | SO4 |
| 5 | 372 | 0.57 | 0.75 | 45 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1827 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1811 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 91 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (artifact, methylation).
Compared structures
- 4O1X · Crystal structure of human thymidylate synthase double mutant C195S-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 4O1X · PDBe 4O1X · UniProt P04818
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