Research workbench
Crystal structure of cytidylate kinase from encephalitozoon cuniculi gb-M1 in complex with two cdp molecules
Analyse Crystal structure of cytidylate kinase from encephalitozoon cuniculi gb-M1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L4A
- Type
- protein
- Length
- 223 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidylate kinase
- EC
- 2.7.4.25
- UniProt
- Q8SS83
- Ligands
- CDP, SO4
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytidylate kinase (EC 2.7.4.25) | protein | 223 | 54% helix, 16% strand | Q8SS83 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.66 | 0.84 | 36 | CDP |
| 2 | 139 | 0.48 | 0.78 | 23 | empty |
Compared structures
- 7L4A · Crystal Structure of Cytidylate kinase from Encephalitozoon cuniculi GB-M1 in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8SS83 · AlphaFold monomer V2.0 prediction for probable cytidylate kinase (Q8SS83) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8SS83
- Elsewhere: RCSB PDB 7L4A · PDBe 7L4A · UniProt Q8SS83
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