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Crystal structure of bace complex with BMC022
Analyse Crystal structure of bace complex with BMC022 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QCU
- Type
- protein
- Length
- 1,130 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
- E51
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 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, C | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 16% helix, 41% strand | P56817 |
Ligands and binding sites
- E51 · (2R,4S)-N-butyl-4-[(5S,8S,10R)-5,10-dimethyl-3,3,6-trioxo-3lambda~6~-thia-7-azabicyclo[11.3.1]heptadeca-1(17),13,15-trien-8-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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.73 | 0.77 | 84 | E51 |
| 2 | 489 | 0.71 | 0.81 | 68 | E51 |
| 3 | 407 | 0.67 | 0.80 | 45 | E51 |
| 4 | 170 | 0.62 | 0.84 | 35 | empty |
| 5 | 131 | 0.50 | 0.79 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1047 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 526 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 5QCU · PDBe 5QCU · UniProt P56817
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