Research workbench
Crystal structure of mycobacterium tuberculosis thymidylate kinase complexed with thymidine-5'-diphosphate (tdp)
Analyse Crystal structure of mycobacterium tuberculosis thymidylate kinase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GTV
- Type
- protein
- Length
- 416 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
- TYD, TMP, MG, SO4
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate kinase (EC 2.7.4.9) | protein | 208 | 45% helix, 52% strand | O05891 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · chains A, B
- TMP · Thymidine-5'-phosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.69 | 0.83 | 78 | MG, TYD, SO4, ACT, TMP |
Interfaces
1 interface between chains.
- A–B · 757 Ų buried · 275 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1GTV · Crystal structure of mycobacterium tuberculosis thymidylate kinase complexed with… · 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 1GTV · PDBe 1GTV · UniProt O05891
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