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X-ray structure of the amyloid precursor protein-like protein 1 (APLP1) E2 domain in complex with a heparin dodecasaccharide
Analyse X-ray structure of the amyloid precursor protein-like protein 1 (APLP1) E2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RDA
- Type
- protein
- Length
- 399 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.497
- Source
- Homo sapiens
- Molecule
- Amyloid-like protein 1
- UniProt
- P51693
- Ligands
- IDS, SGN, UAP, ZN
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.497 · 2 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amyloid-like protein 1 | protein | 203 | 85% helix, 0% strand | P51693 |
| B | Amyloid-like protein 1 | protein | 196 | 88% helix, 0% strand | P51693 |
Ligands and binding sites
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 5 copies · chains A, B
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 5 copies · chains A, B
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · sugar · chains A, B
- ZN · Zinc ion · metal · chains A
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 | 650 | 0.63 | 0.73 | 57 | IDS, SGN, UAP |
| 2 | 197 | 0.57 | 0.80 | 25 | empty |
| 3 | 63 | 0.32 | 0.75 | 15 | empty |
| 4 | 67 | 0.31 | 0.75 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1973 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4RDA · X-ray structure of the amyloid precursor protein-like protein 1 (APLP1) E2 domain in… · 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 0.92
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 4RDA · PDBe 4RDA · UniProt P51693
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