MolNFT v1 · #30256 · protein
Crystal structure of the catalytic domain of an adenosine deaminase that acts on RNA (HADAR2) bound to inositol hexakisphosphate (ihp)
1ZY7 · RNA-specific adenosine deaminase B1, isoform DRADA2A: “Crystal structure of the catalytic domain of an adenosine deaminase that acts on RNA (HADAR2) bound to…”. X-ray diffraction, 3 ligands (IHP, ZN, SO4), 7 pockets (best…
- 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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