MolNFT v1 · #145852 · protein + RNA
Human ADAR2D E488Y mutant complexed with dsrna containing an abasic site opposite the edited base
6D06 · Double-stranded RNA-specific editase 1: “Human ADAR2D E488Y mutant complexed with dsrna containing an abasic site opposite the edited base”. X-ray diffraction, 2 ligands (IHP, ZN), 14 pockets (best druggability 0.83). MolNFT v1…
- 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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