MolNFT v1 · #166488 · protein
Crystal structure of broadly neutralizing antibody AR3X in complex with hepatitis C virus envelope glycoprotein E2 ectodomain
6URH · HCV envelope glycoprotein E2: “Crystal structure of broadly neutralizing antibody AR3X in complex with hepatitis C virus envelope…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 8 pockets (best druggability 0.52). MolNFT v1 #166488…
- PDB
- 6URH
- Type
- protein
- Length
- 616 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV envelope glycoprotein E2; AR3X heavy chain; AR3X light chain
- UniProt
- A0A2P0NE21
- Ligands
- NAG, MAN, BMA
- Pockets
- 8 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | HCV envelope glycoprotein E2 | protein | 161 | 15% helix, 35% strand | A0A2P0NE21 |
| H | AR3X heavy chain | protein | 242 | 9% helix, 50% strand | — |
| L | AR3X light chain | protein | 213 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains C, H, L
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains C
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.52 | 0.74 | 44 | empty |
| 2 | 185 | 0.50 | 0.77 | 42 | empty |
| 3 | 57 | 0.48 | 0.86 | 23 | empty |
| 4 | 123 | 0.47 | 0.79 | 22 | empty |
| 5 | 151 | 0.43 | 0.75 | 27 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1820 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 1208 Ų buried · 15 hydrogen bonds · protein-protein
- C–L · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6URH · Crystal structure of broadly neutralizing antibody AR3X in complex with Hepatitis C virus… · 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 A0A2P0NE21
- Elsewhere: RCSB PDB 6URH · PDBe 6URH · UniProt A0A2P0NE21
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