Research workbench
Crystal structure of GP2 from lassa virus in a post fusion conformation
Analyse Crystal structure of GP2 from lassa virus in a 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
- 5OMI
- Type
- protein
- Length
- 325 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-glycoprotein polyprotein gp complex
- UniProt
- A0A097F3Y1
- Ligands
- NAG, NA, CL
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-glycoprotein polyprotein gp complex | protein | 107 | 72% helix, 2% strand | A0A097F3Y1 |
| B | Pre-glycoprotein polyprotein gp complex | protein | 108 | 73% helix, 2% strand | A0A097F3Y1 |
| C | Pre-glycoprotein polyprotein gp complex | protein | 110 | 69% helix, 2% strand | A0A097F3Y1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- NA · Sodium ion · metal · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.52 | 0.77 | 27 | empty |
| 2 | 203 | 0.52 | 0.77 | 38 | empty |
| 3 | 95 | 0.44 | 0.79 | 19 | empty |
| 4 | 101 | 0.43 | 0.78 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1805 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1729 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1700 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5OMI · Crystal structure of GP2 from Lassa virus in a 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 A0A097F3Y1
- Elsewhere: RCSB PDB 5OMI · PDBe 5OMI · UniProt A0A097F3Y1
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