MolNFT v1 · #99229 · protein
Crystal structure of human beta secretase in complex with compound 11A
4LXA · Beta-secretase 1: “Crystal structure of human beta secretase in complex with compound 11A”. X-ray diffraction, 2 ligands (1YS, PO4), 8 pockets (best druggability 0.78). MolNFT v1 #99229 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4LXA
- Type
- protein
- Length
- 1,135 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 1YS, PO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 376 | 15% helix, 41% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 378 | 15% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 381 | 15% helix, 39% strand | P56817 |
Ligands and binding sites
- 1YS · (1R,3S,4S,5R)-3-{4-amino-3-fluoro-5-[(1,1,1,3,3,3-hexafluoropropan-2-yl)oxy]benzyl}-5-[(3-tert-butylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1-oxide · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.78 | 0.80 | 119 | 1YS |
| 2 | 645 | 0.72 | 0.79 | 67 | 1YS |
| 3 | 133 | 0.56 | 0.83 | 25 | empty |
| 4 | 110 | 0.46 | 0.79 | 27 | empty |
| 5 | 130 | 0.44 | 0.76 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1028 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 571 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
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 P56817
- Elsewhere: RCSB PDB 4LXA · PDBe 4LXA · UniProt P56817
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