Research workbench
Crystal structure of broadly neutralizing antibody HEPC74 in complex with hepatitis C virus envelope glycoprotein E2 ectodomain
Analyse Crystal structure of broadly neutralizing antibody HEPC74 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MEH
- Type
- protein
- Length
- 603 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E2 glycoprotein; Antibody HEPC74 heavy chain; Antibody HEPC74 light chain
- UniProt
- A0A2P0NE26
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | E2 glycoprotein | protein | 165 | 14% helix, 38% strand | A0A2P0NE26 |
| H | Antibody HEPC74 heavy chain | protein | 225 | 8% helix, 54% strand | — |
| L | Antibody HEPC74 light chain | protein | 213 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.60 | 0.75 | 51 | empty |
| 2 | 96 | 0.58 | 0.87 | 32 | empty |
| 3 | 172 | 0.49 | 0.77 | 37 | empty |
| 4 | 118 | 0.40 | 0.74 | 18 | empty |
| 5 | 86 | 0.39 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1964 Ų buried · 18 hydrogen bonds · protein-protein
- C–H · 1031 Ų buried · 10 hydrogen bonds · protein-protein
- C–L · 111 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6MEH · Crystal structure of broadly neutralizing antibody HEPC74 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 6MEH · PDBe 6MEH · UniProt A0A2P0NE26
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