Research workbench
GP1 receptor-binding domain from whitewater arroyo mammarenavirus
Analyse GP1 receptor-binding domain from whitewater arroyo mammarenavirus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NSJ
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-glycoprotein polyprotein gp complex
- UniProt
- Q911P0
- Ligands
- NAG, MAN, SM
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pre-glycoprotein polyprotein gp complex | protein | 142 | 27% helix, 25% strand | Q911P0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar
- SM · Samarium (III) ion · metal · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.76 | 0.97 | 19 | empty |
| 2 | 122 | 0.50 | 0.80 | 33 | SM |
Interfaces
1 interface between chains.
- A–B · 574 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5NSJ · GP1 receptor-binding domain from Whitewater Arroyo mammarenavirus · 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 Q911P0
- Elsewhere: RCSB PDB 5NSJ · PDBe 5NSJ · UniProt Q911P0
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