Research workbench
2.25 ångström resolution crystal structure of a thymidylate kinase (tmk) from vibrio cholerae O1 biovar eltor str. N16961 in complex with thymidine
Analyse 2.25 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
- 3N2I
- Type
- protein
- Length
- 415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q9KQI2
- Ligands
- THM, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 206 | 57% helix, 13% strand | Q9KQI2 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 209 | 56% helix, 12% strand | Q9KQI2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.73 | 0.91 | 26 | THM |
| 2 | 246 | 0.70 | 0.85 | 42 | CL, THM |
| 3 | 84 | 0.51 | 0.84 | 19 | empty |
| 4 | 115 | 0.49 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1220 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3N2I · 2.25 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 B 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 3N2I · PDBe 3N2I · UniProt Q9KQI2
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