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CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH Pep#3

Analyse CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH Pep#3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5MBW
Type
protein
Length
399 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
2.95
Source
Homo sapiens; SYNTHETIC CONSTRUCT
Molecule
Beta-secretase 1; BACE1 INHIBITOR PEPTIDE Pep#3
EC
3.4.23.46
UniProt
P56817
Ligands
CL
Pockets
1 · best druggability 0.57

Structure

x-ray diffraction · resolution 2.95 · 2 distinct chains · 16% helix, 39% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ABeta-secretase 1 (EC 3.4.23.46)protein39016% helix, 40% strandP56817
BBACE1 INHIBITOR PEPTIDE Pep#3protein90% helix, 22% strand—

Ligands and binding sites

  • CL · Chloride ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11100.570.8526empty

Interfaces

1 interface between chains.

  • A–B · 892 Ų buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 d-amino, 1 modified (disulfide, D-amino acid, nonstandard).

Compared structures

  • 5MBW · Crystal structure of bace-1 in complex with PEP#3 · 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 0.99

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