Research workbench
Crystal structure of human beta-secretase in complex with nvp-AFJ144
Analyse Crystal structure of human beta-secretase in complex with nvp-AFJ144 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DUY
- Type
- protein
- Length
- 1,114 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
- AFJ
- Pockets
- 7 · best druggability 0.75
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 | 370 | 16% helix, 41% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 370 | 16% helix, 42% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 374 | 16% helix, 40% strand | P56817 |
Ligands and binding sites
- AFJ · (2R,4S,5S)-N-butyl-4-hydroxy-2,7-dimethyl-5-{[N-(4-methylpentanoyl)-L-methionyl]amino}octanamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.75 | 0.78 | 105 | AFJ |
| 2 | 567 | 0.73 | 0.81 | 71 | AFJ |
| 3 | 531 | 0.72 | 0.81 | 66 | AFJ |
| 4 | 161 | 0.57 | 0.82 | 26 | empty |
| 5 | 177 | 0.47 | 0.76 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1071 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 471 Ų buried · 11 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 3DUY · PDBe 3DUY · UniProt P56817
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