Research workbench
Crystal structure of the ntd L199M of drosophila oskar protein
Analyse Crystal structure of the ntd L199M of drosophila oskar protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CD7
- Type
- protein
- Length
- 433 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maternal effect protein oskar
- UniProt
- P25158
- Pockets
- 1 · best druggability 0.25
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maternal effect protein oskar | protein | 77 | 36% helix, 16% strand | P25158 |
| B | Maternal effect protein oskar | protein | 72 | 42% helix, 15% strand | P25158 |
| C | Maternal effect protein oskar | protein | 75 | 45% helix, 16% strand | P25158 |
| D | Maternal effect protein oskar | protein | 73 | 40% helix, 16% strand | P25158 |
| E | Maternal effect protein oskar | protein | 68 | 41% helix, 16% strand | P25158 |
| F | Maternal effect protein oskar | protein | 68 | 44% helix, 16% strand | P25158 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.25 | 0.73 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 697 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 674 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 619 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 600 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 493 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 5CD7 · Crystal structure of the NTD L199M of Drosophila Oskar protein · the same entry in another collection · chain F against F, TM-score 1.00
- P25158 · AlphaFold monomer V2.0 prediction for maternal effect protein oskar (P25158) · a predicted model of the same protein · chain D 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 P25158
- Elsewhere: RCSB PDB 5CD7 · PDBe 5CD7 · UniProt P25158
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