Research workbench
Structure of sosuga virus receptor binding protein
Analyse Structure of sosuga virus receptor binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SG8
- Type
- protein
- Length
- 751 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-neuraminidase
- UniProt
- W5SB61
- Ligands
- NAG, CA
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin-neuraminidase | protein | 370 | 5% helix, 55% strand | W5SB61 |
| B | Hemagglutinin-neuraminidase | protein | 381 | 5% helix, 55% strand | W5SB61 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.77 | 0.82 | 82 | ACT |
| 2 | 304 | 0.65 | 0.81 | 36 | empty |
| 3 | 272 | 0.63 | 0.81 | 24 | empty |
| 4 | 191 | 0.54 | 0.79 | 30 | ACT |
| 5 | 163 | 0.50 | 0.78 | 31 | ACT |
Interfaces
1 interface between chains.
- A–B · 1412 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6SG8 · Structure of Sosuga virus receptor binding 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 W5SB61
- Elsewhere: RCSB PDB 6SG8 · PDBe 6SG8 · UniProt W5SB61
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