Research workbench
Crystal structure of hepatitis C virus envelope glycoprotein E2 ectodomain in complex with human antibodies HEPC3 and HEPC46
Analyse Crystal structure of hepatitis C virus envelope glycoprotein E2 ectodomain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MEJ
- Type
- protein
- Length
- 1,099 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody HEPC46 heavy chain; Antibody HEPC46 light chain; E2 glycoprotein; Antibody HEPC3…
- UniProt
- C1KH25
- Ligands
- NAG, MAN, BMA
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody HEPC46 heavy chain | protein | 215 | 8% helix, 52% strand | — |
| B | Antibody HEPC46 light chain | protein | 212 | 8% helix, 49% strand | — |
| C | E2 glycoprotein | protein | 234 | 15% helix, 27% strand | C1KH25 |
| H | Antibody HEPC3 heavy chain | protein | 225 | 8% helix, 55% strand | — |
| L | Antibody HEPC3 light chain | protein | 213 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, H, L, A
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.68 | 0.79 | 62 | empty |
| 2 | 163 | 0.67 | 0.87 | 28 | empty |
| 3 | 213 | 0.59 | 0.80 | 36 | empty |
| 4 | 359 | 0.57 | 0.75 | 42 | empty |
| 5 | 346 | 0.56 | 0.75 | 41 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1967 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1719 Ų buried · 14 hydrogen bonds · protein-protein
- C–H · 1076 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 673 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 198 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6MEJ · Crystal structure of Hepatitis C virus envelope glycoprotein E2 ectodomain in complex… · 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 C1KH25
- Elsewhere: RCSB PDB 6MEJ · PDBe 6MEJ · UniProt C1KH25
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