Research workbench
The cross-reaction complex structure with vqifnk peptide and the tau ANTIBODY'S Fab domain.
Analyse The cross-reaction complex structure with vqifnk peptide and the tau ANTIBODY'S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FGR
- Type
- protein
- Length
- 437 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain; Vqifnk
- Ligands
- CL, NH4, IOD
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain | protein | 214 | 8% helix, 53% strand | — |
| L | Fab light chain | protein | 217 | 7% helix, 55% strand | — |
| C | Vqifnk | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains H, L
- NH4 · Ammonium ion · ion · 2 copies · chains H
- IOD · Iodide ion · ion · chains H, L
- GOL · Glycerol · additive · 5 copies · chains H, L
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 | 379 | 0.56 | 0.74 | 45 | GOL |
| 2 | 84 | 0.34 | 0.75 | 23 | empty |
| 3 | 70 | 0.31 | 0.74 | 15 | empty |
| 4 | 62 | 0.28 | 0.73 | 17 | IOD |
| 5 | 68 | 0.27 | 0.72 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1874 Ų buried · 18 hydrogen bonds · protein-protein
- L–C · 329 Ų buried · 8 hydrogen bonds · protein-protein
- H–C · 232 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7FGR · The cross-reaction complex structure with VQIFNK peptide and the tau antibody's Fab… · 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 7FGR · PDBe 7FGR
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