MolNFT v1 · #71912 · protein
Structure of bace (beta secretase) in complex with inhibitor
3MSJ · Beta-secretase 1: “Structure of bace (beta secretase) in complex with inhibitor”. X-ray diffraction, 1 ligand (EV3), 7 pockets (best druggability 0.80). MolNFT v1 #71912 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MSJ
- Type
- protein
- Length
- 1,121 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- EV3
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 373 | 15% helix, 42% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 373 | 14% helix, 43% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 14% helix, 42% strand | P56817 |
Ligands and binding sites
- EV3 · 3-(2-amino-5-chloro-1H-benzimidazol-1-yl)propan-1-ol · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 17 copies · chains A, B, C
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 | 1110 | 0.80 | 0.81 | 114 | EV3, GOL |
| 2 | 559 | 0.68 | 0.78 | 61 | EV3, GOL |
| 3 | 113 | 0.58 | 0.85 | 22 | empty |
| 4 | 97 | 0.55 | 0.85 | 33 | empty |
| 5 | 163 | 0.44 | 0.75 | 23 | GOL |
Interfaces
2 interfaces between chains.
- B–C · 810 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 619 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 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 P56817
- Elsewhere: RCSB PDB 3MSJ · PDBe 3MSJ · UniProt P56817
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