MolNFT v1 · #27553 · protein
Crystal structure of beta-secretase bound to a long inhibitor with additional upstream residues.
1XN3 · Beta-secretase 1: “Crystal structure of beta-secretase bound to a long inhibitor with additional upstream residues.”. X-ray diffraction, 11 pockets (best druggability 0.80). MolNFT v1 #27553 on GenesisL1: 3D structure, binding sites…
- PDB
- 1XN3
- Type
- protein
- Length
- 1,570 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1; Peptidic inhibitor
- EC
- 3.4.23.46
- UniProt
- P56817
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-secretase 1 (EC 3.4.23.46) | protein | 389 | 15% helix, 40% strand | P56817 |
| I | Peptidic inhibitor | protein | 14 | 0% helix, 14% strand | — |
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.80 | 0.81 | 101 | empty |
| 2 | 403 | 0.67 | 0.80 | 43 | empty |
| 3 | 386 | 0.65 | 0.79 | 44 | empty |
| 4 | 466 | 0.63 | 0.77 | 48 | empty |
| 5 | 304 | 0.63 | 0.80 | 35 | empty |
Interfaces
7 interfaces between chains.
- C–I · 1121 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 554 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 248 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 137 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 1XN3 · Crystal structure of Beta-secretase bound to a long inhibitor with additional upstream… · the same entry in another collection · chain I against I, TM-score 1.00
- P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain D against A, TM-score 1.00
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 1XN3 · PDBe 1XN3 · UniProt P56817
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