Research workbench
Crystal structure of puumala virus gc in complex with Fab 4G2
Analyse Crystal structure of puumala virus gc in complex with Fab 4G2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z06
- Type
- protein
- Length
- 847 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 4G2 heavy chain; Fab 4G2 light chain; Envelope polyprotein
- UniProt
- Q9WJ31
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab 4G2 heavy chain | protein | 212 | 3% helix, 51% strand | — |
| L | Fab 4G2 light chain | protein | 213 | 4% helix, 50% strand | — |
| A | Envelope polyprotein | protein | 422 | 3% helix, 52% strand | Q9WJ31 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · 3 copies · chains L, A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.64 | 0.84 | 24 | empty |
| 2 | 515 | 0.60 | 0.74 | 50 | empty |
| 3 | 251 | 0.58 | 0.78 | 35 | GOL |
| 4 | 291 | 0.57 | 0.77 | 36 | empty |
| 5 | 108 | 0.43 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1565 Ų buried · 11 hydrogen bonds · protein-protein
- L–A · 496 Ų buried · 3 hydrogen bonds · protein-protein
- H–A · 411 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6Z06 · Crystal structure of Puumala virus Gc in complex with Fab 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 6Z06 · PDBe 6Z06 · UniProt Q9WJ31
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