MolNFT v1 · #131723 · protein
Crystal structure of bace complex with BMC021
5QCW · Beta-secretase 1: “Crystal structure of bace complex with BMC021”. X-ray diffraction, 1 ligand (AR9), 5 pockets (best druggability 0.76). MolNFT v1 #131723 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QCW
- Type
- protein
- Length
- 1,136 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
- AR9
- Pockets
- 5 · best druggability 0.76
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 | 377 | 16% helix, 41% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 378 | 15% helix, 40% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 381 | 16% helix, 39% strand | P56817 |
Ligands and binding sites
- AR9 · (2R,4S)-N-butyl-4-[(2S,5S,7R)-2,7-dimethyl-3,15-dioxo-1,4-diazacyclopentadecan-5-yl]-4-hydroxy-2-methylbutanamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.76 | 0.79 | 103 | AR9 |
| 2 | 511 | 0.74 | 0.82 | 68 | AR9 |
| 3 | 499 | 0.72 | 0.81 | 70 | AR9 |
| 4 | 346 | 0.64 | 0.79 | 49 | empty |
| 5 | 56 | 0.45 | 0.84 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1081 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 467 Ų buried · 6 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 5QCW · PDBe 5QCW · UniProt P56817
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