Research workbench
Mtb tmk crystal structure in complex with compound 33
Analyse Mtb tmk crystal structure in complex with compound 33 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NRQ
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- P9WKE1
- Ligands
- ZUI, CL
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 190 | 55% helix, 13% strand | P9WKE1 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 184 | 54% helix, 14% strand | P9WKE1 |
Ligands and binding sites
- ZUI · 1-[1-[[5-(3-chloranylphenoxy)pyridin-3-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.58 | 0.81 | 24 | ZUI |
| 2 | 160 | 0.53 | 0.79 | 21 | ZUI |
| 3 | 133 | 0.40 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 16 hydrogen bonds · protein-protein
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 P9WKE1
- Elsewhere: RCSB PDB 5NRQ · PDBe 5NRQ · UniProt P9WKE1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.