Research workbench
Structure of editosome protein
Analyse Structure of editosome protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DKA
- Type
- protein
- Length
- 422 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single domain antibody vhh; RNA-editing complex protein MP81
- UniProt
- Q95W15
- Ligands
- NA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Single domain antibody vhh | protein | 127 | 9% helix, 50% strand | — |
| C | RNA-editing complex protein MP81 | protein | 86 | 0% helix, 64% strand | Q95W15 |
| D | RNA-editing complex protein MP81 | protein | 82 | 0% helix, 66% strand | Q95W15 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.61 | 0.77 | 49 | empty |
| 2 | 183 | 0.48 | 0.76 | 26 | empty |
| 3 | 107 | 0.37 | 0.74 | 31 | empty |
| 4 | 56 | 0.25 | 0.73 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–D · 864 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 309 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 246 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 225 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 216 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4DKA · Structure of Editosome protein · the same entry in another collection · chain A 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 Q95W15
- Elsewhere: RCSB PDB 4DKA · PDBe 4DKA · UniProt Q95W15
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