2.2 ångström crystal structure of cytidine deaminase from vibrio cholerae in complex with zinc and uridine

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).

Ligands and binding sites

• URI · Uridine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
• ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
• MG · Magnesium ion · metal · chains B, E
• ACT · Acetate ion · additive · 9 copies · chains A, B, D, E, F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Interfaces

12 interfaces between chains.

• A–B · 2011 Ų buried · 34 hydrogen bonds · protein-protein
• E–F · 1999 Ų buried · 34 hydrogen bonds · protein-protein
• C–D · 1979 Ų buried · 31 hydrogen bonds · protein-protein
• G–H · 1955 Ų buried · 33 hydrogen bonds · protein-protein
• A–C · 919 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 88 modified (engineered).

Compared structures

• 4EG2 · 2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with… · the same entry in another collection · chain H against H, TM-score 1.00
• Q9KSM5 · AlphaFold monomer V2.0 prediction for cytidine deaminase (Q9KSM5) · a predicted model of the same protein · chain G 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 Q9KSM5
• Elsewhere: RCSB PDB 4EG2 · PDBe 4EG2 · UniProt Q9KSM5