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Crystal structure of human beta secretase in complex with compound 11D
Analyse Crystal structure of human beta secretase in complex with compound 11D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LXK
- 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
- 1YT
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 376 | 16% helix, 40% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 378 | 16% helix, 42% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 381 | 16% helix, 39% strand | P56817 |
Ligands and binding sites
- 1YT · (1R,3S,4S,5R)-3-(4-amino-3-fluoro-5-{[(2R)-1,1,1-trifluoro-3-methoxypropan-2-yl]oxy}benzyl)-5-[(3-tert-butylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1-oxide · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.74 | 0.77 | 97 | 1YT |
| 2 | 497 | 0.69 | 0.79 | 46 | 1YT |
| 3 | 447 | 0.65 | 0.78 | 40 | 1YT |
| 4 | 163 | 0.59 | 0.82 | 30 | empty |
| 5 | 132 | 0.57 | 0.83 | 30 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1035 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 577 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 4LXK · PDBe 4LXK · UniProt P56817
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