MolNFT v1 · #131736 · protein
Crystal structure of bace complex with BMC005
5QD9 · Beta-secretase 1: “Crystal structure of bace complex with BMC005”. X-ray diffraction, 1 ligand (E6Y), 8 pockets (best druggability 0.75). MolNFT v1 #131736 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QD9
- Type
- protein
- Length
- 1,132 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
- E6Y
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 15% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 378 | 16% helix, 39% strand | P56817 |
Ligands and binding sites
- E6Y · (5S,8S,10R)-8-[(1R)-2-{[1-(3-tert-butylphenyl) cyclopropyl]amino}-1-hydroxyethyl]-4,5,10-trimethyl-1-oxa-4,7-diazacyclohexadecane-3,6-dione · ligand · 3 copies · chains A, B, C
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 | 1026 | 0.75 | 0.78 | 101 | E6Y |
| 2 | 537 | 0.71 | 0.80 | 64 | E6Y |
| 3 | 575 | 0.71 | 0.79 | 69 | E6Y |
| 4 | 109 | 0.48 | 0.80 | 22 | empty |
| 5 | 158 | 0.45 | 0.75 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1064 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 597 Ų buried · 8 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 5QD9 · PDBe 5QD9 · UniProt P56817
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