Research workbench
1.8 ångström resolution crystal structure of a thymidylate kinase (tmk) from vibrio cholerae O1 biovar eltor str. N16961 in complex with tmp, thymidine-5'-diphosphate and ADP
Analyse 1.8 ångström resolution crystal structure of a thymidylate kinase (tmk) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LV8
- Type
- protein
- Length
- 204 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q9KQI2
- Ligands
- ADP, TMP, TYD, CA, CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 204 | 55% helix, 13% strand | Q9KQI2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- TMP · Thymidine-5'-phosphate · ligand · chains A
- TYD · Thymidine-5'-diphosphate · ligand · chains A
- CA · Calcium ion · metal · 6 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.67 | 0.87 | 21 | TMP, TYD, CA |
| 2 | 104 | 0.54 | 0.83 | 21 | empty |
Compared structures
- 3LV8 · 1.8 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KQI2 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q9KQI2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9KQI2
- Elsewhere: RCSB PDB 3LV8 · PDBe 3LV8 · UniProt Q9KQI2
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