Research workbench
Schmallenberg virus glycoprotein gc HEAD/STALK domains
Analyse Schmallenberg virus glycoprotein gc HEAD/STALK domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H3S
- Type
- protein
- Length
- 816 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelopment polyprotein
- UniProt
- H2AM12
- Ligands
- NAG, SO4, CL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Envelopment polyprotein | protein | 408 | 38% helix, 18% strand | H2AM12 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
- SO4 · Sulfate ion · ion · 11 copies · chains B, A
- CL · Chloride ion · ion · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.82 | 0.83 | 119 | CL, SO4 |
| 2 | 470 | 0.74 | 0.83 | 53 | SO4 |
| 3 | 100 | 0.44 | 0.79 | 25 | empty |
| 4 | 127 | 0.42 | 0.75 | 17 | empty |
| 5 | 57 | 0.37 | 0.80 | 13 | CL |
Interfaces
1 interface between chains.
- B–A · 1437 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6H3S · Schmallenberg Virus Glycoprotein Gc Head/Stalk Domains · the same entry in another collection · chain B against B, 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 6H3S · PDBe 6H3S · UniProt H2AM12
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