Research workbench
Crystal structure of TAP01 in complex with cyclised amyloid beta peptide
Analyse Crystal structure of TAP01 in complex with cyclised amyloid beta peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OXN
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TAP01 family antibody heavy chain; TAP01 family antibody light chain; Amyloid-beta…
- UniProt
- P05067
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | TAP01 family antibody heavy chain | protein | 214 | 7% helix, 52% strand | — |
| K | TAP01 family antibody light chain | protein | 213 | 5% helix, 50% strand | — |
| A | Amyloid-beta precursor protein | protein | 14 | 0% helix, 36% strand | P05067 |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.56 | 0.79 | 36 | empty |
| 2 | 297 | 0.52 | 0.74 | 41 | empty |
| 3 | 84 | 0.36 | 0.76 | 24 | EDO |
| 4 | 81 | 0.35 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–K · 1827 Ų buried · 8 hydrogen bonds · protein-protein
- K–A · 379 Ų buried · 7 hydrogen bonds · protein-protein
- H–A · 345 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, methylation).
Compared structures
- 7OXN · Crystal Structure of TAP01 in complex with cyclised amyloid beta peptide · the same entry in another collection · chain H against H, TM-score 1.00
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain A against A, TM-score 0.42
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 P05067
- Elsewhere: RCSB PDB 7OXN · PDBe 7OXN · UniProt P05067
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