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Puumala virus glycoprotein (gc) in complex with Fab fragment P-4G2.
Analyse Puumala virus glycoprotein (gc) in complex with Fab fragment P-4G2. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B09
- Type
- protein
- Length
- 1,178 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab fragment P-4G2; Light chain of Fab fragment P-4G2; Envelope polyprotein
- UniProt
- Q9WJ31
- Ligands
- NAG, BMA, MAN
- Pockets
- 12 · best druggability 0.77
Structure
electron microscopy · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of Fab fragment P-4G2 | protein | 212 | 3% helix, 51% strand | — |
| L | Light chain of Fab fragment P-4G2 | protein | 213 | 4% helix, 50% strand | — |
| A | Envelope polyprotein | protein | 422 | 3% helix, 52% strand | Q9WJ31 |
| B | Envelope polyprotein | protein | 331 | 11% helix, 47% strand | Q9WJ31 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.77 | 0.79 | 119 | empty |
| 2 | 502 | 0.66 | 0.78 | 57 | empty |
| 3 | 190 | 0.64 | 0.84 | 24 | empty |
| 4 | 561 | 0.60 | 0.74 | 57 | empty |
| 5 | 75 | 0.43 | 0.80 | 22 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1561 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1313 Ų buried · 29 hydrogen bonds · protein-protein
- L–A · 494 Ų buried · 3 hydrogen bonds · protein-protein
- H–A · 413 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7B09 · Puumala virus glycoprotein (Gc) in complex with fab fragment P-4G2. · the same entry in another collection · chain H against H, 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 Q9WJ31
- Elsewhere: RCSB PDB 7B09 · PDBe 7B09 · UniProt Q9WJ31
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