Research workbench
Antibody-anti-idiotype complex: AP33 Fab (hepatitis C virus E2 antibody) - B2.1A scfv (anti-idiotype)
Analyse Antibody-anti-idiotype complex: AP33 Fab (hepatitis C virus E2 antibody)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SXI
- Type
- protein
- Length
- 654 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain; Single chain fv - heavy chain; Single chain fv - light…
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain | protein | 212 | 6% helix, 54% strand | — |
| L | Fab light chain | protein | 215 | 6% helix, 53% strand | — |
| A | Single chain fv - heavy chain | protein | 119 | 10% helix, 50% strand | — |
| B | Single chain fv - light chain | protein | 108 | 3% helix, 46% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.65 | 0.75 | 64 | empty |
| 2 | 96 | 0.54 | 0.84 | 21 | empty |
| 3 | 109 | 0.36 | 0.73 | 23 | GOL |
| 4 | 66 | 0.30 | 0.74 | 18 | empty |
| 5 | 71 | 0.29 | 0.73 | 17 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1908 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 934 Ų buried · 8 hydrogen bonds · protein-protein
- H–A · 398 Ų buried · 2 hydrogen bonds · protein-protein
- L–A · 383 Ų buried · 6 hydrogen bonds · protein-protein
- L–B · 252 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6SXI · Antibody-anti-idiotype complex: AP33 Fab (hepatitis C virus E2 antibody) - B2.1A scFv… · the same entry in another collection · chain H against H, 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 6SXI · PDBe 6SXI
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