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Crystal structure of a plant cytidine deaminase
Analyse Crystal structure of a plant cytidine deaminase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JFY
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxycytidine deaminase
- UniProt
- H2EMX8
- Ligands
- ZN, CL
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxycytidine deaminase | protein | 119 | 39% helix, 26% strand | H2EMX8 |
| C | Deoxycytidine deaminase | protein | 121 | 39% helix, 26% strand | H2EMX8 |
| D | Deoxycytidine deaminase | protein | 117 | 39% helix, 24% strand | H2EMX8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 4 copies · chains A, C, B
- GOL · Glycerol · additive · 3 copies · chains A, C
- HEZ · Hexane-1,6-diol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.45 | 0.74 | 36 | ACT, GOL |
| 2 | 68 | 0.33 | 0.76 | 15 | empty |
| 3 | 57 | 0.27 | 0.73 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1073 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 879 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 838 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 91 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 83 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5JFY · Crystal structure of a plant cytidine deaminase · the same entry in another collection · 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 H2EMX8
- Elsewhere: RCSB PDB 5JFY · PDBe 5JFY · UniProt H2EMX8
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