Research workbench
Structure of the anti-ptau Fab (PT231/PS235_1) in complex with phosphoepitope PT231/PS235
Analyse Structure of the anti-ptau Fab (PT231/PS235_1) in complex with phosphoepitope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GLR
- Type
- protein
- Length
- 891 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-peptide; Anti-ptau heavy chain; Anti-ptau light chain
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospho-peptide | protein | 10 | 0% helix, 0% strand | — |
| H | Anti-ptau heavy chain | protein | 229 | 8% helix, 49% strand | — |
| I, K | Anti-ptau light chain | protein | 207 | 6% helix, 52% strand | — |
| J | Anti-ptau heavy chain | protein | 228 | 7% helix, 49% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains H, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.69 | 0.79 | 56 | empty |
| 2 | 471 | 0.60 | 0.74 | 55 | empty |
| 3 | 309 | 0.53 | 0.75 | 49 | empty |
| 4 | 132 | 0.47 | 0.78 | 31 | PO4 |
| 5 | 76 | 0.42 | 0.80 | 18 | empty |
Interfaces
9 interfaces between chains.
- H–I · 1829 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 1806 Ų buried · 20 hydrogen bonds · protein-protein
- A–H · 485 Ų buried · 14 hydrogen bonds · protein-protein
- B–J · 456 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 393 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 modified (disulfide, phosphorylation).
Compared structures
- 4GLR · Structure of the anti-ptau Fab (pT231/pS235_1) in complex with phosphoepitope pT231/pS235 · 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 4GLR · PDBe 4GLR
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