MolNFT v1 · #127465 · protein
Bace-1 in complex with ligand 32397778
5MXD · Beta-secretase 1: “Bace-1 in complex with ligand 32397778”. X-ray diffraction, 2 ligands (III, CL), 9 pockets (best druggability 0.82). MolNFT v1 #127465 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MXD
- Type
- protein
- Length
- 1,140 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
- III, CL
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 390 | 15% helix, 38% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 370 | 15% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 380 | 14% helix, 41% strand | P56817 |
Ligands and binding sites
- III · ~{N},~{N}-dimethyl-2-pyrrolidin-1-yl-quinazolin-4-amine · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.82 | 0.83 | 98 | III |
| 2 | 51 | 0.63 | 0.94 | 22 | empty |
| 3 | 479 | 0.62 | 0.76 | 43 | III, CL |
| 4 | 89 | 0.55 | 0.85 | 29 | empty |
| 5 | 180 | 0.46 | 0.75 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1001 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 634 Ų buried · 14 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 5MXD · PDBe 5MXD · UniProt P56817
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