Research workbench
Structure of hepatitis C virus envelope glycoprotein E2MC3-V1 redesigned core from genotype 1A bound to broadly neutralizing antibody AR3C
Analyse Structure of hepatitis C virus envelope glycoprotein E2MC3-V1 redesigned core… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UYD
- Type
- protein
- Length
- 1,168 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
- 11 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Envelope glycoprotein E2 | protein | 143 | 13% helix, 38% strand | — |
| H | Fab AR3C heavy chain | protein | 222 | 7% helix, 52% strand | — |
| L | Fab AR3C light chain | protein | 211 | 6% helix, 50% strand | — |
| A | Fab AR3C heavy chain | protein | 222 | 7% helix, 53% strand | — |
| B | Fab AR3C light chain | protein | 212 | 6% helix, 51% strand | — |
| F | Envelope glycoprotein E2 | protein | 158 | 11% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains E, F, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.64 | 0.74 | 73 | empty |
| 2 | 608 | 0.63 | 0.75 | 71 | empty |
| 3 | 187 | 0.51 | 0.77 | 27 | empty |
| 4 | 113 | 0.50 | 0.81 | 24 | empty |
| 5 | 188 | 0.48 | 0.76 | 33 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1867 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1787 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 693 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 682 Ų buried · 9 hydrogen bonds · protein-protein
- E–A · 476 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6UYD · Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 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 6UYD · PDBe 6UYD
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