Research workbench
Structure of the lotus domain of oskar in complex with the C-terminal reca-like domain of vasa
Analyse Structure of the lotus domain of oskar in complex with the C-terminal reca-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NT7
- Type
- protein
- Length
- 490 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase vasa, isoform a; Maternal effect protein oskar
- EC
- 3.6.4.13
- UniProt
- P09052, P25158
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | ATP-dependent RNA helicase vasa, isoform a (EC 3.6.4.13) | protein | 153 | 44% helix, 20% strand | P09052 |
| A, C | Maternal effect protein oskar | protein | 92 | 46% helix, 12% strand | P25158 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.62 | 0.82 | 34 | empty |
| 2 | 188 | 0.59 | 0.81 | 24 | empty |
| 3 | 73 | 0.37 | 0.78 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1139 Ų buried · 18 hydrogen bonds · protein-protein
- B–A · 1122 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 722 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5NT7 · Structure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain of… · the same entry in another collection · chain B against B, TM-score 1.00
- P09052 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase vasa (P09052) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P25158 · AlphaFold monomer V2.0 prediction for maternal effect protein oskar (P25158) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P09052
- Every structure of UniProt P25158
- Elsewhere: RCSB PDB 5NT7 · PDBe 5NT7 · UniProt P09052 · UniProt P25158
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