MolNFT v1 · #86728 · protein
BACE2 xaperone complex
4BFB · Beta-secretase 2: “BACE2 xaperone complex”. X-ray diffraction, 6 pockets (best druggability 0.74). MolNFT v1 #86728 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4BFB
- Type
- protein
- Length
- 978 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 2; XA4813
- EC
- 3.4.23.45
- UniProt
- Q9Y5Z0
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 2 (EC 3.4.23.45) | protein | 373 | 14% helix, 42% strand | Q9Y5Z0 |
| B | Beta-secretase 2 (EC 3.4.23.45) | protein | 374 | 13% helix, 42% strand | Q9Y5Z0 |
| D | XA4813 | protein | 110 | 11% helix, 52% strand | — |
| E | XA4813 | protein | 121 | 7% helix, 47% strand | — |
Ligands and binding sites
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.74 | 0.77 | 100 | empty |
| 2 | 492 | 0.67 | 0.78 | 44 | empty |
| 3 | 519 | 0.67 | 0.77 | 40 | B3P |
| 4 | 172 | 0.60 | 0.83 | 30 | empty |
| 5 | 149 | 0.44 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–E · 854 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 848 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 773 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 491 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 132 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 4BFB · PDBe 4BFB · UniProt Q9Y5Z0
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