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Crystal structure of bace complex with BMC016
Analyse Crystal structure of bace complex with BMC016 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QCO
- Type
- protein
- Length
- 1,132 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
- E4A
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 15% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 378 | 15% helix, 40% strand | P56817 |
Ligands and binding sites
- E4A · (4S)-19-acetyl-4-[(1R)-1-hydroxy-2-({1-[3-(propan-2-yl)phenyl]cyclopropyl}amino)ethyl]-11-oxa-3,16-diazatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9, 17,19-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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.73 | 0.77 | 107 | E4A |
| 2 | 567 | 0.70 | 0.79 | 63 | E4A |
| 3 | 562 | 0.69 | 0.78 | 63 | E4A |
| 4 | 158 | 0.58 | 0.83 | 33 | empty |
| 5 | 175 | 0.47 | 0.76 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1076 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 585 Ų buried · 8 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 5QCO · PDBe 5QCO · UniProt P56817
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