Research workbench
Crystal structure of human thymidylate synthase (hts) variant R175C
Analyse Crystal structure of human thymidylate synthase (hts) variant R175C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QYQ
- Type
- protein
- Length
- 1,150 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
- FFO, SO4, CL
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 33% helix, 23% strand | P04818 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 285 | 35% helix, 23% strand | P04818 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 289 | 34% helix, 23% strand | P04818 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 290 | 34% helix, 23% strand | P04818 |
Ligands and binding sites
- FFO · N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.78 | 0.85 | 63 | SO4, FFO |
| 2 | 597 | 0.78 | 0.84 | 64 | SO4, FFO |
| 3 | 544 | 0.71 | 0.79 | 61 | SO4 |
| 4 | 578 | 0.70 | 0.79 | 59 | SO4 |
| 5 | 236 | 0.56 | 0.78 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1653 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1611 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 125 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (artifact, oxidation, methylation).
Compared structures
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 6QYQ · PDBe 6QYQ · UniProt P04818
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