Research workbench
Crystal structure of arabidopsis cytidine deaminase
Analyse Crystal structure of arabidopsis cytidine deaminase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L08
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidine deaminase 1
- EC
- 3.5.4.5
- UniProt
- O65896
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytidine deaminase 1 (EC 3.5.4.5) | protein | 285 | 29% helix, 12% strand | O65896 |
| B | Cytidine deaminase 1 (EC 3.5.4.5) | protein | 284 | 29% helix, 14% strand | O65896 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.76 | 0.97 | 21 | empty |
| 2 | 92 | 0.75 | 0.97 | 22 | empty |
| 3 | 73 | 0.73 | 0.97 | 16 | empty |
| 4 | 103 | 0.69 | 0.92 | 34 | empty |
| 5 | 121 | 0.64 | 0.87 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2194 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
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 O65896
- Elsewhere: RCSB PDB 6L08 · PDBe 6L08 · UniProt O65896
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