Research workbench
Structure of hepatitis C virus envelope glycoprotein E2 core from genotype 6A bound to broadly neutralizing antibody RM11-43
Analyse Structure of hepatitis C virus envelope glycoprotein E2 core from genotype 6A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JTG
- Type
- protein
- Length
- 582 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RM11-43 Fab heavy chain; RM11-43 Fab light chain; Envelope glycoprotein E2
- UniProt
- B9V0E2
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RM11-43 Fab heavy chain | protein | 224 | 7% helix, 51% strand | — |
| B | RM11-43 Fab light chain | protein | 212 | 6% helix, 52% strand | — |
| E | Envelope glycoprotein E2 | protein | 146 | 14% helix, 34% strand | B9V0E2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.49 | 0.75 | 31 | empty |
| 2 | 96 | 0.48 | 0.81 | 14 | empty |
| 3 | 116 | 0.36 | 0.73 | 25 | empty |
| 4 | 86 | 0.35 | 0.75 | 18 | empty |
| 5 | 54 | 0.28 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1685 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 764 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 98 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7JTG · Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to… · the same entry in another collection · chain A against A, 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 B9V0E2
- Elsewhere: RCSB PDB 7JTG · PDBe 7JTG · UniProt B9V0E2
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