Research workbench
Structure of bace bound to 2-imino-3-methyl-5,5-diphenylimidazolidin- 4-one
Analyse Structure of bace bound to 2-imino-3-methyl-5,5-diphenylimidazolidin- 4-one in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DJU
- Type
- protein
- Length
- 779 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 0KK
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 390 | 16% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 16% helix, 39% strand | P56817 |
Ligands and binding sites
- 0KK · (2E)-2-imino-3-methyl-5,5-diphenylimidazolidin-4-one · ligand · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.66 | 0.77 | 38 | 0KK |
| 2 | 497 | 0.65 | 0.77 | 42 | 0KK |
| 3 | 78 | 0.56 | 0.87 | 25 | empty |
| 4 | 102 | 0.54 | 0.84 | 31 | empty |
| 5 | 150 | 0.48 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 276 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4DJU · Structure of BACE Bound to 2-imino-3-methyl-5,5-diphenylimidazolidin-4-one · the same entry in another collection · chain A against A, TM-score 1.00
- P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 4DJU · PDBe 4DJU · UniProt P56817
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