Research workbench
Crystal structure of E2 domain of human amyloid precursor-like protein 1
Analyse Crystal structure of E2 domain of human amyloid precursor-like protein 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PMR
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid-like protein 1
- UniProt
- P51693
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amyloid-like protein 1 | protein | 195 | 86% helix, 0% strand | P51693 |
| B | Amyloid-like protein 1 | protein | 198 | 88% helix, 0% strand | P51693 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
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 | 663 | 0.63 | 0.73 | 57 | PO4 |
| 2 | 192 | 0.62 | 0.82 | 20 | empty |
| 3 | 177 | 0.49 | 0.76 | 25 | empty |
| 4 | 57 | 0.27 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1910 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3PMR · Crystal Structure of E2 domain of Human Amyloid Precursor-Like Protein 1 · the same entry in another collection · chain A against A, TM-score 1.00
- P51693 · AlphaFold monomer V2.0 prediction for amyloid-like protein 1 (P51693) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P51693
- Elsewhere: RCSB PDB 3PMR · PDBe 3PMR · UniProt P51693
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