Research workbench
The complex structure of phf core domain peptide of tau, vqivyk, and ANTIBODY'S Fab domain.
Analyse The complex structure of phf core domain peptide of tau, vqivyk, and ANTIBODY'S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FGL
- Type
- protein
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain; Vqivyk
- Ligands
- NH4
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain | protein | 219 | 8% helix, 51% strand | — |
| L | Fab light chain | protein | 219 | 7% helix, 54% strand | — |
| C | Vqivyk | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 328 | 0.54 | 0.75 | 35 | empty |
| 2 | 93 | 0.36 | 0.75 | 20 | empty |
| 3 | 91 | 0.33 | 0.73 | 19 | GOL |
| 4 | 51 | 0.31 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1971 Ų buried · 17 hydrogen bonds · protein-protein
- L–C · 294 Ų buried · 9 hydrogen bonds · protein-protein
- H–C · 256 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7FGL · The complex structure of PHF core domain peptide of tau, VQIVYK, and 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 7FGL · PDBe 7FGL
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