MolNFT v1 · #154327 · protein
Crystal structure of thymidylate synthase from shrimp
6K7S: “Crystal structure of thymidylate synthase from shrimp”. X-ray diffraction, 2 ligands (UMP, D16), 6 pockets (best druggability 0.78). MolNFT v1 #154327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6K7S
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- C6GJB8
- Ligands
- UMP, D16
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 278 | 32% helix, 24% strand | C6GJB8 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 34% helix, 23% strand | C6GJB8 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- D16 · Tomudex · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.78 | 0.85 | 49 | UMP, D16 |
| 2 | 523 | 0.74 | 0.82 | 47 | UMP, D16 |
| 3 | 100 | 0.41 | 0.77 | 16 | empty |
| 4 | 67 | 0.35 | 0.77 | 14 | empty |
| 5 | 61 | 0.32 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2089 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6K7S · Crystal structure of thymidylate synthase from shrimp · the same entry in another collection · chain B against B, 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 C6GJB8
- Elsewhere: RCSB PDB 6K7S · PDBe 6K7S · UniProt C6GJB8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.