Research workbench
Crystal structure of cytidine deaminase from bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine
Analyse Crystal structure of cytidine deaminase from bacillus subtilis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JTK
- Type
- protein
- Length
- 262 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidine deaminase
- EC
- 3.5.4.5
- UniProt
- P19079
- Ligands
- THU, ZN
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytidine deaminase (EC 3.5.4.5) | protein | 131 | 34% helix, 25% strand | P19079 |
Ligands and binding sites
- THU · Tetrahydrodeoxyuridine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.61 | 0.78 | 33 | THU |
| 2 | 347 | 0.61 | 0.77 | 34 | THU |
| 3 | 76 | 0.33 | 0.75 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 704 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1JTK · Crystal structure of cytidine deaminase from Bacillus subtilis in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P19079 · AlphaFold monomer V2.0 prediction for cytidine deaminase (P19079) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P19079
- Elsewhere: RCSB PDB 1JTK · PDBe 1JTK · UniProt P19079
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