Research workbench
Human ADAR2D E488Y mutant complexed with dsrna containing an abasic site opposite the edited base
Analyse Human ADAR2D E488Y mutant complexed with dsrna containing an abasic site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D06
- Type
- protein + RNA
- Length
- 782 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(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8A…
- EC
- 3.5.4.37
- UniProt
- P78563
- Ligands
- IHP, ZN
- Pockets
- 14 · 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 | 34% helix, 16% strand | P78563 |
| B | RNA (5'-R(*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 | RNA (5'- R(*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*NP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP* C)-3') | rna | 23 | — | — |
| D | Double-stranded RNA-specific editase 1 (EC 3.5.4.37) | protein | 352 | 33% helix, 18% 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
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.83 | 0.92 | 41 | IHP |
| 2 | 492 | 0.81 | 0.88 | 55 | IHP |
| 3 | 635 | 0.72 | 0.80 | 68 | empty |
| 4 | 511 | 0.61 | 0.76 | 29 | empty |
| 5 | 155 | 0.59 | 0.83 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1135 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1073 Ų buried · 117 hydrogen bonds · nucleic-nucleic
- A–B · 793 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 734 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–D · 47 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6D06 · Human ADAR2d E488Y mutant complexed with dsRNA containing an abasic site opposite the… · 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 6D06 · PDBe 6D06 · UniProt P78563
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