Research workbench
Crystal structure of S. aureus thymidylate kinase complexed with thymidine monophosphate
Analyse Crystal structure of S. aureus thymidylate kinase complexed with thymidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CCJ
- Type
- protein
- Length
- 391 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
- TMP, CL
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 196 | 59% helix, 14% strand | P65248 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 195 | 58% helix, 13% strand | P65248 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 3 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.58 | 0.80 | 26 | TMP, EDO |
| 2 | 188 | 0.49 | 0.76 | 31 | TMP |
Interfaces
1 interface between chains.
- A–B · 1012 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2CCJ · Crystal structure of S. aureus thymidylate kinase complexed with thymidine monophosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P65248 · AlphaFold monomer V2.0 prediction for thymidylate kinase (P65248) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 2CCJ · PDBe 2CCJ · UniProt P65248
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