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Crystal structure of bace complex WITHBMC006
Analyse Crystal structure of bace complex WITHBMC006 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QD0
- Type
- protein
- Length
- 1,120 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
- E5Y
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 373 | 16% helix, 42% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 372 | 16% helix, 41% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 375 | 15% helix, 41% strand | P56817 |
Ligands and binding sites
- E5Y · (5S,8S,10R)-8-[(1R)-1-hydroxy-2-{[(5-propyl-1H-pyrazol-3-yl)methyl]amino}ethyl]-4,5,10-trimethyl-1-oxa-4,7-diazacyclohexadecane-3,6-dione · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.74 | 0.77 | 101 | E5Y |
| 2 | 552 | 0.71 | 0.80 | 66 | E5Y |
| 3 | 454 | 0.71 | 0.81 | 57 | E5Y |
| 4 | 352 | 0.63 | 0.79 | 47 | empty |
| 5 | 66 | 0.51 | 0.86 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1064 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 571 Ų buried · 10 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 5QD0 · PDBe 5QD0 · UniProt P56817
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