MolNFT v1 · #128414 · protein
Structure of the hepatitis C virus strain J4 glycoprotein E2 antigenic region 532-540 bound to the single chain variable fragment of the non-neutralizing antibody DAO5
5NPI: “Structure of the hepatitis C virus strain J4 glycoprotein E2 antigenic region 532-540 bound to the single…”. X-ray diffraction, 4 pockets (best druggability 0.67). MolNFT v1 #128414 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NPI
- Type
- protein
- Length
- 485 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single chain variable fragment of the non-neutralizing antibody DAO5; Epitope peptide
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single chain variable fragment of the non-neutralizing antibody DAO5 | protein | 232 | 5% helix, 51% strand | — |
| B | Single chain variable fragment of the non-neutralizing antibody DAO5 | protein | 233 | 5% helix, 51% strand | — |
| E | Epitope peptide | protein | 11 | 45% helix, 0% strand | — |
| D | Epitope peptide | protein | 9 | 56% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.67 | 0.79 | 56 | empty |
| 2 | 109 | 0.37 | 0.74 | 17 | empty |
| 3 | 93 | 0.34 | 0.74 | 19 | empty |
| 4 | 53 | 0.25 | 0.72 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1064 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 683 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 624 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5NPI · Structure of the Hepatitis C virus strain J4 glycoprotein E2 antigenic region 532-540… · 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 5NPI · PDBe 5NPI
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