MolNFT v1 · #81438 · protein
Crystal structure of BACE1 with its inhibitor
3UQP · Beta-secretase 1: “Crystal structure of BACE1 with its inhibitor”. X-ray diffraction, 2 ligands (BOC, SO4), 1 pocket (best druggability 0.38). MolNFT v1 #81438 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UQP
- Type
- protein
- Length
- 381 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1; Methyl (2R)-1-[(6S,9S,12S,13S,17S,20S,23R)-9-(3-amino-3…
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- BOC, SO4
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 374 | 16% helix, 41% strand | P56817 |
| B | Methyl (2R)-1-[(6S,9S,12S,13S,17S,20S,23R)-9-(3-amino-3- oxopropyl)-12,23-dibenzyl-13-hydroxy-2,2,8,20,22-pentamethyl-17-(2- methylpropyl)-4,7,10,15,18,21,24-heptaoxo-6-(propan-2-yl)-3-oxa-5,8, 11,16,19,22-hexaazatetracosan-24-YL]PYRROLIDINE-2-carboxylate | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- BOC · Tert-butyl hydrogen carbonate · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.38 | 0.74 | 18 | BOC |
Interfaces
1 interface between chains.
- A–B · 764 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 3 disulfide, 1 covalent (nonstandard, disulfide, covalent ligand).
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 3UQP · PDBe 3UQP · UniProt P56817
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