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Structure of beta-secretase complexed with inhibitor
Analyse Structure of beta-secretase complexed with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GID
- Type
- protein
- Length
- 1,549 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- 0GH, LPD
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Beta-secretase 1 (EC 3.4.23.46) | protein | 387 | 15% helix, 39% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 388 | 14% helix, 38% strand | P56817 |
Ligands and binding sites
- 0GH · N-[(2S)-1-({(2S,3R)-3-hydroxy-1-[(2-methylpropyl)amino]-1-oxobutan-2-yl}amino)-3-phenylpropan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide · ligand · 4 copies · chains A, B, C, D
- LPD · L-prolinamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.72 | 0.84 | 29 | empty |
| 2 | 389 | 0.71 | 0.83 | 33 | empty |
| 3 | 312 | 0.69 | 0.83 | 46 | 0GH |
| 4 | 334 | 0.69 | 0.82 | 47 | 0GH |
| 5 | 383 | 0.68 | 0.81 | 59 | 0GH |
Interfaces
3 interfaces between chains.
- A–C · 880 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 831 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 86 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 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 4GID · PDBe 4GID · UniProt P56817
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