Research workbench
Structure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2 residues 411-424)
Analyse Structure of the broadly neutralizing antibody AP33 in complex with its HCV… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GAJ
- Type
- protein
- Length
- 434 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutralizing antibody AP33 heavy chain; Neutralizing antibody AP33 light chain; Genome…
- UniProt
- Q9IY15
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Neutralizing antibody AP33 heavy chain | protein | 209 | 4% helix, 55% strand | — |
| L | Neutralizing antibody AP33 light chain | protein | 215 | 4% helix, 49% strand | — |
| P | Genome polyprotein | protein | 10 | 0% helix, 60% strand | Q9IY15 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.67 | 0.75 | 65 | empty |
| 2 | 56 | 0.50 | 0.86 | 12 | empty |
| 3 | 70 | 0.31 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1799 Ų buried · 14 hydrogen bonds · protein-protein
- L–P · 336 Ų buried · 7 hydrogen bonds · protein-protein
- H–P · 327 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4GAJ · Structure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2… · the same entry in another collection · chain L against L, 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 Q9IY15
- Elsewhere: RCSB PDB 4GAJ · PDBe 4GAJ · UniProt Q9IY15
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