Research workbench
Three dimensional structure of broadly neutralizing anti - hepatitis C virus (HCV) glycoprotein E2 alpaca nanobody D03
Analyse Three dimensional structure of broadly neutralizing anti - hepatitis C virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JVP
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-HCV E2 alpaca nanobody D03
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-HCV E2 alpaca nanobody D03 | protein | 131 | 8% helix, 49% strand | — |
| B | Anti-HCV E2 alpaca nanobody D03 | protein | 127 | 9% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.51 | 0.85 | 16 | empty |
| 2 | 142 | 0.46 | 0.77 | 20 | SO4 |
| 3 | 110 | 0.44 | 0.78 | 21 | SO4 |
| 4 | 109 | 0.44 | 0.78 | 23 | empty |
| 5 | 55 | 0.24 | 0.72 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 729 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4JVP · Three dimensional structure of broadly neutralizing anti - Hepatitis C virus (HCV)… · 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
- Elsewhere: RCSB PDB 4JVP · PDBe 4JVP
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