MolNFT v1 · #117601 · protein + RNA
Human adenosine deaminase acting on dsrna (ADAR2) mutant E488Q bound to dsrna sequence derived from human GLI1 gene
5ED2 · Double-stranded RNA-specific editase 1: “Human adenosine deaminase acting on dsrna (ADAR2) mutant E488Q bound to dsrna sequence derived from human…”. X-ray diffraction, 2 ligands (IHP, ZN), 13 pockets (best druggability 0.83).…
- PDB
- 5ED2
- Type
- protein + RNA
- Length
- 862 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double-stranded RNA-specific editase 1; RNA (5'-R(P*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8…
- EC
- 3.5.4.37
- UniProt
- P78563
- Ligands
- IHP, ZN
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Double-stranded RNA-specific editase 1 (EC 3.5.4.37) | protein | 385 | 32% helix, 16% strand | P78563 |
| B, E | RNA (5'-R(P*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ) P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3') | rna | 23 | — | — |
| C, F | RNA (5'- R(P*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP *C)-3') | rna | 23 | — | — |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.83 | 0.91 | 44 | IHP |
| 2 | 381 | 0.82 | 0.91 | 45 | IHP |
| 3 | 99 | 0.75 | 0.96 | 29 | empty |
| 4 | 298 | 0.69 | 0.84 | 47 | empty |
| 5 | 546 | 0.64 | 0.76 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1063 Ų buried · 110 hydrogen bonds · nucleic-nucleic
- E–F · 1058 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- D–E · 834 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 822 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–C · 706 Ų buried · 24 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5ED2 · Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence… · the same entry in another collection · chain C against C, 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 A against A, TM-score 0.96
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 5ED2 · PDBe 5ED2 · UniProt P78563
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