Research workbench
Crystal structure of the catalytic domain of an adenosine deaminase that acts on RNA (HADAR2) bound to inositol hexakisphosphate (ihp)
Analyse Crystal structure of the catalytic domain of an adenosine deaminase that acts… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZY7
- Type
- protein
- Length
- 740 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-specific adenosine deaminase B1, isoform DRADA2A
- UniProt
- P78563
- Ligands
- IHP, ZN, SO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-specific adenosine deaminase B1, isoform DRADA2A | protein | 378 | 35% helix, 17% strand | P78563 |
| B | RNA-specific adenosine deaminase B1, isoform DRADA2A | protein | 362 | 35% helix, 16% strand | P78563 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.83 | 0.86 | 83 | IHP |
| 2 | 413 | 0.82 | 0.90 | 42 | IHP |
| 3 | 504 | 0.70 | 0.80 | 35 | empty |
| 4 | 242 | 0.59 | 0.80 | 45 | empty |
| 5 | 209 | 0.49 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 634 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1ZY7 · Crystal structure of the catalytic domain of an adenosine deaminase that acts on RNA… · the same entry in another collection · chain A against A, TM-score 1.00
- P78563 · AlphaFold monomer V2.0 prediction for double-stranded RNA-specific editase 1 (P78563) · a predicted model of the same protein · chain B 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 P78563
- Elsewhere: RCSB PDB 1ZY7 · PDBe 1ZY7 · UniProt P78563
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