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Structure of human adenosine deaminase acting on dsrna (ADAR2) bound to dsrna containing a 2'-deoxy BENNER'S base Z opposite the edited base
Analyse Structure of human adenosine deaminase acting on dsrna (ADAR2) 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
- 7KFN
- Type
- protein + RNA
- Length
- 785 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double-stranded RNA-specific editase 1; GLI1 8AZ 23MER RNA; GLI1 1W5 23MER RNA
- EC
- 3.5.4.37
- UniProt
- P78563
- Ligands
- IHP, ZN
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double-stranded RNA-specific editase 1 (EC 3.5.4.37) | protein | 384 | 33% helix, 16% strand | P78563 |
| B | GLI1 8AZ 23MER RNA | rna | 23 | — | — |
| C | GLI1 1W5 23MER RNA | rna | 23 | — | — |
| D | Double-stranded RNA-specific editase 1 (EC 3.5.4.37) | protein | 355 | 34% helix, 17% 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.83 | 0.92 | 41 | IHP |
| 2 | 440 | 0.82 | 0.90 | 43 | IHP |
| 3 | 1162 | 0.74 | 0.77 | 91 | empty |
| 4 | 359 | 0.70 | 0.83 | 40 | empty |
| 5 | 495 | 0.60 | 0.75 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1180 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1089 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- A–B · 777 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 691 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–D · 22 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7KFN · Structure of Human Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA containing… · 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 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 7KFN · PDBe 7KFN · UniProt P78563
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