MolNFT v1 · #108782 · protein
Structure of the hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody 3/11, P21 crystal form
4WHY · Epitope peptide: “Structure of the hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly…”. X-ray diffraction, 20 pockets (best druggability 0.72). MolNFT v1 #108782 on GenesisL1: 3D structure…
- PDB
- 4WHY
- Type
- protein
- Length
- 1,709 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epitope peptide; Heavy chain of Fab fragment derived from neutralizing antibody 3/11…
- UniProt
- Q9WJJ4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Epitope peptide | protein | 11 | 0% helix, 0% strand | Q9WJJ4 |
| G | Heavy chain of Fab fragment derived from neutralizing antibody 3/11 | protein | 199 | 6% helix, 54% strand | — |
| H, J, N | Light chain of Fab fragment derived from neutralizing antibody 3/11 | protein | 215 | 6% helix, 49% strand | — |
| I | Heavy chain of Fab fragment derived from neutralizing antibody 3/11 | protein | 203 | 6% helix, 54% strand | — |
| K | Heavy chain of Fab fragment derived from neutralizing antibody 3/11 | protein | 200 | 5% helix, 55% strand | — |
| L | Light chain of Fab fragment derived from neutralizing antibody 3/11 | protein | 218 | 6% helix, 50% strand | — |
| M | Heavy chain of Fab fragment derived from neutralizing antibody 3/11 | protein | 200 | 6% helix, 55% strand | — |
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.72 | 0.78 | 75 | empty |
| 2 | 741 | 0.69 | 0.77 | 70 | empty |
| 3 | 379 | 0.64 | 0.79 | 50 | empty |
| 4 | 635 | 0.63 | 0.74 | 63 | empty |
| 5 | 305 | 0.61 | 0.79 | 42 | empty |
Interfaces
24 interfaces between chains.
- K–L · 1597 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1530 Ų buried · 14 hydrogen bonds · protein-protein
- M–N · 1529 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 1521 Ų buried · 12 hydrogen bonds · protein-protein
- B–M · 477 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4WHY · Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423… · 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 Q9WJJ4
- Elsewhere: RCSB PDB 4WHY · PDBe 4WHY · UniProt Q9WJJ4
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