MolNFT v1 · #156760 · protein
Crystal structure of broadly neutralizing antibody HEPC3 in complex with hepatitis C virus envelope glycoprotein E2 ectodomain
6MEI · E2 glycoprotein: “Crystal structure of broadly neutralizing antibody HEPC3 in complex with hepatitis C virus envelope…”. X-ray diffraction, 3 ligands (NAG, BMA, BR), 10 pockets (best druggability 0.60). MolNFT v1 #156760 on…
- PDB
- 6MEI
- Type
- protein
- Length
- 680 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E2 glycoprotein; Antibody HEPC3 heavy chain; Antibody HEPC3 light chain
- UniProt
- A0A2P0NE26
- Ligands
- NAG, BMA, BR
- Pockets
- 10 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | E2 glycoprotein | protein | 238 | 14% helix, 26% strand | A0A2P0NE26 |
| H | Antibody HEPC3 heavy chain | protein | 228 | 8% helix, 51% strand | — |
| L | Antibody HEPC3 light chain | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains C, H, L
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains L
- BR · Bromide ion · ion · 7 copies · chains C, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.60 | 0.80 | 32 | BR |
| 2 | 54 | 0.59 | 0.92 | 19 | empty |
| 3 | 279 | 0.58 | 0.78 | 36 | empty |
| 4 | 259 | 0.54 | 0.76 | 39 | empty |
| 5 | 107 | 0.45 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2209 Ų buried · 19 hydrogen bonds · protein-protein
- C–H · 1019 Ų buried · 16 hydrogen bonds · protein-protein
- C–L · 89 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6MEI · Crystal structure of broadly neutralizing antibody HEPC3 in complex with Hepatitis C… · the same entry in another collection · chain C against C, 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 A0A2P0NE26
- Elsewhere: RCSB PDB 6MEI · PDBe 6MEI · UniProt A0A2P0NE26
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