MolNFT v1 · #117600 · protein + RNA
Human adenosine deaminase acting on dsrna (ADAR2) mutant E488Q bound to dsrna sequence derived from S. cerevisiae BDF2 gene
5ED1 · Double-stranded RNA-specific editase 1: “Human adenosine deaminase acting on dsrna (ADAR2) mutant E488Q bound to dsrna sequence derived from S.…”. X-ray diffraction, 2 ligands (IHP, ZN), 15 pockets (best druggability 0.83). MolNFT…
- 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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