Research workbench
Crystal structure of unliganded S. aureus thymidylate kinase
Analyse Crystal structure of unliganded S. aureus thymidylate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CCK
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- P65248
- Ligands
- CL
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 192 | 60% helix, 14% strand | P65248 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 192 | 60% helix, 14% strand | P65248 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.51 | 0.78 | 17 | empty |
| 2 | 150 | 0.50 | 0.79 | 24 | empty |
| 3 | 52 | 0.24 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1059 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 P65248
- Elsewhere: RCSB PDB 2CCK · PDBe 2CCK · UniProt P65248
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