Research workbench
Crystal Structure of Guanarito virus GP2 in the post-fusion conformation
Analyse Crystal Structure of Guanarito virus GP2 in the post-fusion conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C53
- Type
- protein
- Length
- 318 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.14
- Source
- GUANARITO VIRUS
- Molecule
- Pre-glycoprotein polyprotein gp complex
- UniProt
- A1A3Z2
- Ligands
- NAG, MAN, BMA
- Pockets
- 5 · best druggability 0.39
Structure
x-ray diffraction · resolution 4.14 · 3 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-glycoprotein polyprotein gp complex | protein | 101 | 63% helix, 2% strand | A1A3Z2 |
| B | Pre-glycoprotein polyprotein gp complex | protein | 115 | 63% helix, 2% strand | A1A3Z2 |
| C | Pre-glycoprotein polyprotein gp complex | protein | 102 | 62% helix, 2% strand | A1A3Z2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 12 copies
- BMA · beta-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.39 | 0.73 | 23 | empty |
| 2 | 100 | 0.37 | 0.74 | 16 | empty |
| 3 | 64 | 0.33 | 0.75 | 14 | empty |
| 4 | 73 | 0.30 | 0.73 | 17 | empty |
| 5 | 50 | 0.26 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2094 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1784 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1745 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan (N-glycosylation).
Compared structures
- 4C53 · Crystal structure of guanarito virus GP2 in the post-fusion conformation · 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 A1A3Z2
- Elsewhere: RCSB PDB 4C53 · PDBe 4C53 · UniProt A1A3Z2
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