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2.2 ångström crystal structure of cytidine deaminase from vibrio cholerae in complex with zinc and uridine
Analyse 2.2 ångström crystal structure of cytidine deaminase from vibrio cholerae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EG2
- Type
- protein
- Length
- 2,374 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidine deaminase
- EC
- 3.5.4.5
- UniProt
- Q9KSM5
- Ligands
- URI, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, H | Cytidine deaminase (EC 3.5.4.5) | protein | 297 | 36% helix, 19% strand | Q9KSM5 |
| C, F | Cytidine deaminase (EC 3.5.4.5) | protein | 296 | 36% helix, 19% strand | Q9KSM5 |
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.84 | 0.85 | 124 | MG |
| 2 | 112 | 0.76 | 0.95 | 21 | URI |
| 3 | 83 | 0.76 | 0.97 | 20 | URI |
| 4 | 82 | 0.75 | 0.97 | 21 | URI |
| 5 | 87 | 0.75 | 0.97 | 22 | URI |
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
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