MolNFT v1 · #89260 · protein
Structure of editosome protein
4DK3 · Single domain antibody vhh: “Structure of editosome protein”. X-ray diffraction, 2 pockets (best druggability 0.65). MolNFT v1 #89260 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DK3
- Type
- protein
- Length
- 417 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
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 57% 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 | 83 | 0% helix, 63% strand | Q95W15 |
| D | RNA-editing complex protein MP81 | protein | 80 | 0% helix, 63% strand | Q95W15 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.65 | 0.77 | 44 | empty |
| 2 | 142 | 0.41 | 0.75 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 972 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 720 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 167 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 74 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4DK3 · 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 4DK3 · PDBe 4DK3 · UniProt Q95W15
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