MolNFT v1 · #105712 · protein
X-ray structure of the amyloid precursor protein-like protein 1 (APLP1) E2 domain in complex with a heparin dodecasaccharide
4RDA · Amyloid-like protein 1: “X-ray structure of the amyloid precursor protein-like protein 1 (APLP1) E2 domain in complex with a heparin…”. X-ray diffraction, 4 ligands (UAP, IDS, SGN), 4 pockets (best druggability 0.63). MolNFT v1…
- PDB
- 4RDA
- Type
- protein
- Length
- 399 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid-like protein 1
- UniProt
- P51693
- Ligands
- UAP, IDS, SGN, ZN
- 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 | 203 | 85% helix, 0% strand | P51693 |
| B | Amyloid-like protein 1 | protein | 196 | 88% helix, 0% strand | P51693 |
Ligands and binding sites
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · ligand · chains A, B
- 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
- 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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