Research workbench
Structure of hepatitis C virus envelope glycoprotein E2MC3-V6 redesigned core from genotype 1A bound to broadly neutralizing antibody AR3C
Analyse Structure of hepatitis C virus envelope glycoprotein E2MC3-V6 redesigned core… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UYM
- Type
- protein
- Length
- 1,145 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein E2; Fab AR3C heavy chain; Fab AR3C light chain
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Envelope glycoprotein E2 | protein | 145 | 12% helix, 35% strand | — |
| H | Fab AR3C heavy chain | protein | 221 | 7% helix, 53% strand | — |
| L | Fab AR3C light chain | protein | 211 | 6% helix, 50% strand | — |
| A | Fab AR3C heavy chain | protein | 223 | 7% helix, 54% strand | — |
| B | Fab AR3C light chain | protein | 208 | 6% helix, 51% strand | — |
| F | Envelope glycoprotein E2 | protein | 137 | 13% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains E, F, H, L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.75 | 0.79 | 66 | empty |
| 2 | 928 | 0.73 | 0.77 | 106 | empty |
| 3 | 592 | 0.62 | 0.74 | 62 | empty |
| 4 | 130 | 0.42 | 0.75 | 24 | empty |
| 5 | 77 | 0.39 | 0.78 | 19 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1788 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1759 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 712 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 699 Ų buried · 7 hydrogen bonds · protein-protein
- H–A · 230 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6UYM · Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v6 redesigned core from… · the same entry in another collection · chain E against E, 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
- Elsewhere: RCSB PDB 6UYM · PDBe 6UYM
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