Research workbench
Structure of hepatitis C virus envelope glycoprotein E2MC3-V1 redesigned core from genotype 6A bound to broadly neutralizing antibody AR3B
Analyse Structure of hepatitis C virus envelope glycoprotein E2MC3-V1 redesigned core… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UYF
- Type
- protein
- Length
- 586 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab AR3B heavy chain; Fab AR3B light chain; Envelope glycoprotein E2
- Ligands
- NAG, BMA, MAN
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab AR3B heavy chain | protein | 218 | 6% helix, 53% strand | — |
| L | Fab AR3B light chain | protein | 214 | 7% helix, 53% strand | — |
| E | Envelope glycoprotein E2 | protein | 154 | 11% helix, 36% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains H, L, E
- 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.54 | 0.74 | 49 | empty |
| 2 | 128 | 0.48 | 0.79 | 26 | empty |
| 3 | 84 | 0.34 | 0.75 | 21 | empty |
| 4 | 61 | 0.33 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1798 Ų buried · 15 hydrogen bonds · protein-protein
- H–E · 828 Ų buried · 10 hydrogen bonds · protein-protein
- L–E · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6UYF · Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from… · 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
- Elsewhere: RCSB PDB 6UYF · PDBe 6UYF
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