MolNFT v1 · #15463 · protein
Crystal structure of mycobacterium tuberculosis thymidylate kinase crystallized in sodium malonate (resolution 2.1 a)
1N5K: “Crystal structure of mycobacterium tuberculosis thymidylate kinase crystallized in sodium malonate…”. X-ray diffraction, 2 ligands (TMP, MG), 4 pockets (best druggability 0.64). MolNFT v1 #15463 on GenesisL1: 3D structure, binding…
- PDB
- 1N5K
- Type
- protein
- Length
- 400 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, MG
- Pockets
- 4 · best druggability 0.64
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 | 196 | 54% helix, 12% strand | O05891 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 204 | 54% helix, 12% strand | O05891 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- ACT · Acetate ion · additive · 3 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 | 119 | 0.64 | 0.88 | 21 | TMP |
| 2 | 287 | 0.64 | 0.81 | 35 | ACT, MG, TMP |
| 3 | 63 | 0.37 | 0.79 | 24 | empty |
| 4 | 83 | 0.34 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 851 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1N5K · 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 1N5K · PDBe 1N5K · UniProt O05891
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