MolNFT v1 · #126766 · protein
Crystal structure of bace-1 in complex with active site and exosite binding peptide inhibitor
5MCQ · Beta-secretase 1: “Crystal structure of bace-1 in complex with active site and exosite binding peptide inhibitor”. X-ray diffraction, 1 ligand (NH2), 3 pockets (best druggability 0.49). MolNFT v1 #126766 on GenesisL1: 3D structure…
- PDB
- 5MCQ
- Type
- protein
- Length
- 414 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1; Bace-1 active and exosite binding inhibitor
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- NH2
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 393 | 15% helix, 41% strand | P56817 |
| D | Bace-1 active and exosite binding inhibitor | protein | 21 | 0% helix, 29% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.49 | 0.78 | 26 | empty |
| 2 | 113 | 0.42 | 0.77 | 23 | empty |
| 3 | 78 | 0.35 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–D · 1391 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 d-amino, 3 disulfide, 1 modified (D-amino acid, disulfide, nonstandard).
Compared structures
- 5MCQ · Crystal structure of bace-1 in complex with active site and exosite binding peptide… · 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 0.96
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 5MCQ · PDBe 5MCQ · UniProt P56817
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