MolNFT v1 · #131737 · protein
Crystal structure of bace complex with BMC013
5QDA · Beta-secretase 1: “Crystal structure of bace complex with BMC013”. X-ray diffraction, 1 ligand (E74), 10 pockets (best druggability 0.74). MolNFT v1 #131737 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QDA
- Type
- protein
- Length
- 1,135 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
- E74
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 16% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 381 | 16% helix, 39% strand | P56817 |
Ligands and binding sites
- E74 · (4S)-4-[(1R)-1-hydroxy-2-({[3-(propan-2-yl) phenyl]methyl}amino)ethyl]-18-methoxy-3,15,17-triazatricyclo[14.3.1.1~6,10~]henicosa-1(20),6(21),7, 9,16,18-hexaen-2-one · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.74 | 0.80 | 79 | E74 |
| 2 | 463 | 0.69 | 0.80 | 46 | E74 |
| 3 | 459 | 0.67 | 0.79 | 43 | E74 |
| 4 | 144 | 0.55 | 0.82 | 34 | empty |
| 5 | 147 | 0.50 | 0.79 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1060 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 5QDA · PDBe 5QDA · UniProt P56817
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