Research workbench
Mtb tmk crystal structure in complex with compound 3
Analyse Mtb tmk crystal structure in complex with compound 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NRN
- Type
- protein
- Length
- 398 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
- 95W, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 187 | 54% helix, 14% strand | P9WKE1 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 211 | 53% helix, 12% strand | P9WKE1 |
Ligands and binding sites
- 95W · 5-methyl-1-[1-[(6-phenoxypyridin-2-yl)methyl]piperidin-4-yl]pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.76 | 0.85 | 42 | 95W, CL |
| 2 | 178 | 0.55 | 0.79 | 20 | 95W |
| 3 | 108 | 0.38 | 0.75 | 18 | empty |
| 4 | 57 | 0.34 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 820 Ų buried · 14 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 5NRN · PDBe 5NRN · UniProt P9WKE1
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