MolNFT v1 · #131718 · protein
Crystal structure of bace complex with BMC026
5QCR · Beta-secretase 1: “Crystal structure of bace complex with BMC026”. X-ray diffraction, 2 ligands (E4J, SO4), 9 pockets (best druggability 0.72). MolNFT v1 #131718 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QCR
- Type
- protein
- Length
- 1,125 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
- E4J, SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 15% helix, 42% strand | P56817 |
Ligands and binding sites
- E4J · 2-(butylamino)-N-[(2S,3S,5R)-6-(butylamino)-3-hydroxy-5-methyl-6-oxo-1-phenylhexan-2-yl]-6-methoxypyridine-4-carboxamide · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.72 | 0.79 | 101 | E4J |
| 2 | 327 | 0.67 | 0.82 | 46 | E4J |
| 3 | 337 | 0.66 | 0.81 | 45 | E4J |
| 4 | 141 | 0.55 | 0.82 | 27 | empty |
| 5 | 117 | 0.52 | 0.82 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1140 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 546 Ų buried · 9 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 5QCR · PDBe 5QCR · UniProt P56817
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