MolNFT v1 · #84429 · protein
BACE2 mutant structure with ligand
3ZKI · Beta-secretase 2: “BACE2 mutant structure with ligand”. X-ray diffraction, 1 ligand (WZV), 4 pockets (best druggability 0.74). MolNFT v1 #84429 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZKI
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 2
- EC
- 3.4.23.45
- UniProt
- Q9Y5Z0
- Ligands
- WZV
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 2 (EC 3.4.23.45) | protein | 365 | 16% helix, 43% strand | Q9Y5Z0 |
| B | Beta-secretase 2 (EC 3.4.23.45) | protein | 361 | 15% helix, 43% strand | Q9Y5Z0 |
Ligands and binding sites
- WZV · 5-(2,2,2-Trifluoro-ethoxy)-pyridine-2-carboxylic acid [3-((S)-2-amino-1,4-dimethyl-6-oxo-1,4,5,6-tetrahydro-pyrimidin-4-yl)-phenyl]-amide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.74 | 0.77 | 71 | WZV |
| 2 | 869 | 0.73 | 0.77 | 73 | WZV |
| 3 | 54 | 0.35 | 0.79 | 16 | empty |
| 4 | 51 | 0.34 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 482 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 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 Q9Y5Z0
- Elsewhere: RCSB PDB 3ZKI · PDBe 3ZKI · UniProt Q9Y5Z0
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