Research workbench
Structure of hepatitis C virus envelope glycoprotein E2 core from genotype 1A bound to neutralizing antibody 212.1.1 and non neutralizing antibody E1
Analyse Structure of hepatitis C virus envelope glycoprotein E2 core from genotype 1A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WO5
- Type
- protein
- Length
- 2,016 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab E1 heavy chain; Fab E1 light chain; Fab 212.1.1 heavy chain; Fab 212.1.1 light chain…
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 10 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab E1 heavy chain | protein | 212 | 6% helix, 51% strand | — |
| B | Fab E1 light chain | protein | 221 | 6% helix, 53% strand | — |
| C | Fab E1 heavy chain | protein | 216 | 4% helix, 51% strand | — |
| D | Fab E1 light chain | protein | 219 | 6% helix, 51% strand | — |
| H | Fab 212.1.1 heavy chain | protein | 219 | 7% helix, 49% strand | — |
| L | Fab 212.1.1 light chain | protein | 212 | 5% helix, 51% strand | — |
| G | Fab 212.1.1 heavy chain | protein | 220 | 8% helix, 49% strand | — |
| I | Fab 212.1.1 light chain | protein | 211 | 6% helix, 52% strand | — |
| E | Envelope glycoprotein E2 | protein | 148 | 12% helix, 31% strand | — |
| F | Envelope glycoprotein E2 | protein | 138 | 7% helix, 36% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains H, E, L, G, F, I, D, A, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains G, I, L
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.66 | 0.75 | 58 | empty |
| 2 | 709 | 0.66 | 0.74 | 67 | empty |
| 3 | 641 | 0.64 | 0.74 | 64 | empty |
| 4 | 589 | 0.62 | 0.74 | 63 | empty |
| 5 | 74 | 0.60 | 0.90 | 22 | empty |
Interfaces
16 interfaces between chains.
- C–D · 1813 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1707 Ų buried · 12 hydrogen bonds · protein-protein
- G–I · 1679 Ų buried · 10 hydrogen bonds · protein-protein
- H–L · 1672 Ų buried · 12 hydrogen bonds · protein-protein
- G–F · 651 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6WO5 · Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 1a bound to… · 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
- Elsewhere: RCSB PDB 6WO5 · PDBe 6WO5
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