MolNFT v1 · #126738 · protein
Crystal structure of bace-1 in complex with PEP#3
5MBW · Beta-secretase 1: “Crystal structure of bace-1 in complex with PEP#3”. X-ray diffraction, 1 ligand (CL), 1 pocket (best druggability 0.57). MolNFT v1 #126738 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MBW
- Type
- protein
- Length
- 399 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1; BACE1 inhibitor peptide PEP#3
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- CL
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 390 | 16% helix, 40% strand | P56817 |
| B | BACE1 inhibitor peptide PEP#3 | protein | 9 | 0% helix, 22% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.57 | 0.85 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 892 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 d-amino, 1 modified (disulfide, D-amino acid, nonstandard).
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 5MBW · PDBe 5MBW · UniProt P56817
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