Research workbench
BACE2 xaperone complex
Analyse BACE2 xaperone complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BEL
- Type
- protein
- Length
- 940 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
- Ligands
- CL
- Pockets
- 6 · best druggability 0.67
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 | 358 | 15% helix, 42% strand | Q9Y5Z0 |
| B | Beta-secretase 2 (EC 3.4.23.45) | protein | 357 | 15% helix, 43% strand | Q9Y5Z0 |
| D | XA4813 | protein | 112 | 8% helix, 52% strand | — |
| E | XA4813 | protein | 113 | 8% helix, 50% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, D
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.67 | 0.78 | 50 | B3P |
| 2 | 486 | 0.67 | 0.78 | 43 | B3P |
| 3 | 180 | 0.52 | 0.78 | 31 | empty |
| 4 | 109 | 0.40 | 0.76 | 17 | empty |
| 5 | 60 | 0.33 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–D · 854 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 772 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 61 Ų buried · 0 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 4BEL · PDBe 4BEL · UniProt Q9Y5Z0
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