Research workbench
Schmallenberg Virus Glycoprotein Gc Head Domain in Complex with scFv 4B6
Analyse Schmallenberg Virus Glycoprotein Gc Head Domain in Complex with scFv 4B6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H3U
- Type
- protein
- Length
- 954 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.168
- Source
- Bovine Schmallenberg virus; Mus musculus
- Molecule
- scFv 4B6 VH; scFv 4B6 VL; Envelopment polyprotein
- UniProt
- H2AM12
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · resolution 3.168 · 6 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | scFv 4B6 VH | protein | 121 | 2% helix, 51% strand | — |
| L | scFv 4B6 VL | protein | 113 | 3% helix, 46% strand | — |
| A | Envelopment polyprotein | protein | 246 | 57% helix, 0% strand | H2AM12 |
| B | Envelopment polyprotein | protein | 245 | 54% helix, 0% strand | H2AM12 |
| M | scFv 4B6 VL | protein | 107 | 3% helix, 47% strand | — |
| I | scFv 4B6 VH | protein | 122 | 2% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.80 | 0.81 | 86 | empty |
| 2 | 1140 | 0.79 | 0.81 | 98 | empty |
| 3 | 220 | 0.60 | 0.81 | 30 | empty |
| 4 | 118 | 0.48 | 0.79 | 15 | empty |
| 5 | 109 | 0.39 | 0.75 | 19 | empty |
Interfaces
9 interfaces between chains.
- H–L · 907 Ų buried · 7 hydrogen bonds · protein-protein
- M–I · 875 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 646 Ų buried · 7 hydrogen bonds · protein-protein
- A–I · 496 Ų buried · 8 hydrogen bonds · protein-protein
- H–B · 494 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6H3U · Schmallenberg virus glycoprotein gc head domain in complex with scfv 4B6 · 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 H2AM12
- Elsewhere: RCSB PDB 6H3U · PDBe 6H3U · UniProt H2AM12
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