Research workbench
Structure of hepatitis C virus envelope glycoprotein E2 core from genotype 1A bound to neutralizing antibody HC1AM 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
- 6WOQ
- Type
- protein
- Length
- 1,940 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab E1 heavy chain; Fab E1 light chain; Envelope glycoprotein E2; Fab HC1AM heavy chain…
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · 9 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab E1 heavy chain | protein | 215 | 4% helix, 51% strand | — |
| B, D | Fab E1 light chain | protein | 217 | 5% helix, 48% strand | — |
| E | Envelope glycoprotein E2 | protein | 137 | 7% helix, 38% strand | — |
| J | Fab HC1AM heavy chain | protein | 218 | 6% helix, 43% strand | — |
| K | Fab HC1AM light chain | protein | 212 | 4% helix, 49% strand | — |
| C | Fab E1 heavy chain | protein | 191 | 2% helix, 51% strand | — |
| F | Envelope glycoprotein E2 | protein | 125 | 10% helix, 39% strand | — |
| G | Fab HC1AM heavy chain | protein | 213 | 6% helix, 46% strand | — |
| H | Fab HC1AM light chain | protein | 195 | 4% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains E, J, K, F, H, A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.63 | 0.74 | 54 | empty |
| 2 | 503 | 0.62 | 0.75 | 57 | empty |
| 3 | 595 | 0.62 | 0.74 | 63 | empty |
| 4 | 397 | 0.57 | 0.75 | 50 | empty |
| 5 | 357 | 0.56 | 0.75 | 41 | empty |
Interfaces
17 interfaces between chains.
- J–K · 1972 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1846 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1841 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1715 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 682 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6WOQ · 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 6WOQ · PDBe 6WOQ
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