Research workbench
Structures of thymidylate synthase R163K with substrates and inhibitors show subunit asymmetry
Analyse Structures of thymidylate synthase R163K with substrates and inhibitors show… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H9K
- Type
- protein
- Length
- 1,404 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- UFP, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Thymidylate synthase (EC 2.1.1.45) | protein | 281 | 36% helix, 24% strand | P04818 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 280 | 31% helix, 24% strand | P04818 |
Ligands and binding sites
- UFP · 5-fluoro-2'-deoxyuridine-5'-monophosphate · ligand · 3 copies · chains A, B, D, E
- PO4 · Phosphate ion · ion · 2 copies · chains C, D, E
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
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 | 1127 | 0.79 | 0.80 | 86 | UFP |
| 2 | 723 | 0.71 | 0.77 | 67 | UFP, EDO |
| 3 | 529 | 0.67 | 0.78 | 47 | PO4 |
| 4 | 555 | 0.67 | 0.77 | 56 | empty |
| 5 | 360 | 0.60 | 0.77 | 45 | PO4 |
Interfaces
6 interfaces between chains.
- A–B · 2289 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2235 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 679 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 283 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3H9K · Structures of Thymidylate Synthase R163K with Substrates and Inhibitors Show Subunit… · 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 3H9K · PDBe 3H9K · UniProt P04818
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.