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Crystal structure of bace complex with BMC023
Analyse Crystal structure of bace complex with BMC023 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QD4
- Type
- protein
- Length
- 1,135 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
- AXQ
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 16% helix, 42% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 381 | 16% helix, 39% strand | P56817 |
Ligands and binding sites
- AXQ · {(E)-(3R,6S,9R)-3-[(1S,3R)-3-((S)-1 -butylcarbamoyl-2-methyl-propylcarb amoyl)-1-hydroxy-butyl]-6-methyl-5, 8-dioxo-1,11-dithia-4,7-diaza-cyclo pentadec-13-en-9-yl}-carbamic acid tert-butyl ester · 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 | 497 | 0.73 | 0.82 | 65 | AXQ |
| 2 | 519 | 0.72 | 0.81 | 67 | AXQ |
| 3 | 587 | 0.70 | 0.79 | 70 | AXQ |
| 4 | 159 | 0.56 | 0.81 | 30 | empty |
| 5 | 126 | 0.51 | 0.81 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1073 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 457 Ų buried · 6 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 5QD4 · PDBe 5QD4 · UniProt P56817
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