Research workbench
Crystal structure of the E2 domain of APLP1 in complex with heparin hexasaccharide
Analyse Crystal structure of the E2 domain of APLP1 in complex with heparin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QMK
- Type
- protein
- Length
- 391 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid-like protein 1
- UniProt
- P51693
- Ligands
- SGN, IDS, SO4
- Pockets
- 4 · best druggability 0.54
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 | 196 | 89% helix, 0% strand | P51693 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains 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 | 258 | 0.54 | 0.76 | 26 | empty |
| 2 | 386 | 0.54 | 0.73 | 42 | IDS, SGN, SO4 |
| 3 | 155 | 0.48 | 0.77 | 22 | empty |
| 4 | 56 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1837 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3QMK · Crystal structure of the E2 domain of APLP1 in complex with heparin hexasaccharide · 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 3QMK · PDBe 3QMK · UniProt P51693
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