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Crystal structure of mycobacterium tuberculosis thymidylate kinase crystallized in sodium malonate, after catalysis in the crystal (2.3 a resolution)
Analyse Crystal structure of mycobacterium tuberculosis thymidylate kinase crystallized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N5L
- 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
- O05891
- Ligands
- TMP, TYD, DPO, MG
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 195 | 54% helix, 13% strand | O05891 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 203 | 53% helix, 12% strand | — |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · chains A
- TYD · Thymidine-5'-diphosphate · ligand · chains B
- DPO · Diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains B
- ACT · Acetate ion · additive · 2 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 | 287 | 0.68 | 0.83 | 36 | MG, TYD, DPO |
| 2 | 161 | 0.57 | 0.82 | 28 | ACT, TMP |
| 3 | 63 | 0.36 | 0.78 | 27 | empty |
| 4 | 100 | 0.34 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 856 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1N5L · Crystal structure of mycobacterium tuberculosis thymidylate kinase crystallized in sodium… · 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 O05891
- Elsewhere: RCSB PDB 1N5L · PDBe 1N5L · UniProt O05891
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