Research workbench
Crystal structure of hepatitis C virus envelope glycoprotein E2 core in complex with human antibodies HEPC3 and HEPC46
Analyse Crystal structure of hepatitis C virus envelope glycoprotein E2 core in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MEK
- Type
- protein
- Length
- 2,044 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E2 glycoprotein; HEPC3 heavy chain; HEPC3 light chain; HEPC46 light chain; HEPC46 heavy…
- UniProt
- H2FJ05
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 9 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E2 glycoprotein | protein | 165 | 10% helix, 35% strand | H2FJ05 |
| B | HEPC3 heavy chain | protein | 224 | 4% helix, 52% strand | — |
| C | E2 glycoprotein | protein | 170 | 12% helix, 34% strand | H2FJ05 |
| D, L | HEPC3 light chain | protein | 213 | 7% helix, 46% strand | — |
| E | HEPC46 light chain | protein | 200 | 2% helix, 40% strand | — |
| F | HEPC46 heavy chain | protein | 210 | 7% helix, 48% strand | — |
| G | HEPC46 light chain | protein | 212 | 8% helix, 46% strand | — |
| H | HEPC3 heavy chain | protein | 222 | 7% helix, 52% strand | — |
| I | HEPC46 heavy chain | protein | 215 | 5% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, D, C, F, I, H, L
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains D
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.61 | 0.85 | 22 | empty |
| 2 | 415 | 0.59 | 0.75 | 52 | empty |
| 3 | 171 | 0.56 | 0.81 | 25 | empty |
| 4 | 377 | 0.56 | 0.75 | 45 | empty |
| 5 | 173 | 0.56 | 0.80 | 35 | empty |
Interfaces
13 interfaces between chains.
- H–L · 2061 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1895 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 1737 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1661 Ų buried · 15 hydrogen bonds · protein-protein
- C–H · 1025 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6MEK · Crystal structure of Hepatitis C virus envelope glycoprotein E2 core in complex with… · the same entry in another collection · chain B against B, 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 H2FJ05
- Elsewhere: RCSB PDB 6MEK · PDBe 6MEK · UniProt H2FJ05
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