Research workbench
Human adenosine deaminase acting on dsrna (ADAR2) mutant E488Q bound to dsrna sequence derived from S. cerevisiae BDF2 gene
Analyse Human adenosine deaminase acting on dsrna (ADAR2) mutant E488Q bound to dsrna… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ED1
- Type
- protein + RNA
- Length
- 839 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double-stranded RNA-specific editase 1; RNA (5'-R(*UP*UP*CP*CP*CP*CP*AP*CP*AP*UP*UP*(8AZ)…
- EC
- 3.5.4.37
- UniProt
- P78563
- Ligands
- IHP, ZN
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double-stranded RNA-specific editase 1 (EC 3.5.4.37) | protein | 396 | 31% helix, 16% strand | P78563 |
| B | RNA (5'-R(*UP*UP*CP*CP*CP*CP*AP*CP*AP*UP*UP*(8AZ) P*GP*AP*CP*GP*UP*UP*CP*AP*GP*UP*C)-3') | rna | 23 | — | — |
| C | RNA (5'- R(*GP*AP*CP*UP*GP*AP*AP*CP*GP*AP*CP*CP*AP*AP*UP*GP*UP*GP*GP*GP*GP*AP* a)-3') | rna | 23 | — | — |
| D | Double-stranded RNA-specific editase 1 (EC 3.5.4.37) | protein | 397 | 32% helix, 16% strand | P78563 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.83 | 0.88 | 58 | empty |
| 2 | 405 | 0.83 | 0.91 | 41 | IHP |
| 3 | 473 | 0.82 | 0.89 | 50 | IHP |
| 4 | 810 | 0.70 | 0.77 | 47 | empty |
| 5 | 310 | 0.69 | 0.84 | 50 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1037 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- A–D · 895 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 783 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–C · 707 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5ED1 · Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence… · 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 D against A, TM-score 0.99
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 5ED1 · PDBe 5ED1 · UniProt P78563
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