MolNFT v1 · #91952 · protein
Crystal structure of beta-site app-cleaving enzyme 1 (bace-db-mut) complex with N-(N-(4- acetamido-3-chloro-5-methylbenzyl) carbamimidoyl)-3-(4- methoxyphenyl)-5-methyl-4-isothiazolecarboxamide
4FSL · Beta-secretase 1: “Crystal structure of beta-site app-cleaving enzyme 1 (bace-db-mut) complex with N-(N-(4…”. X-ray diffraction, 2 ligands (0VB, IOD), 15 pockets (best druggability 0.73). MolNFT v1 #91952 on GenesisL1: 3D structure…
- PDB
- 4FSL
- Type
- protein
- Length
- 1,548 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
- 0VB, IOD
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Beta-secretase 1 (EC 3.4.23.46) | protein | 387 | 16% helix, 39% strand | P56817 |
Ligands and binding sites
- 0VB · N-{N-[4-(acetylamino)-3-chloro-5-methylbenzyl]carbamimidoyl}-3-(4-methoxyphenyl)-5-methyl-1,2-thiazole-4-carboxamide · ligand · 4 copies · chains A, B, D, E
- IOD · Iodide ion · ion · 12 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.73 | 0.83 | 43 | empty |
| 2 | 411 | 0.73 | 0.84 | 31 | empty |
| 3 | 468 | 0.69 | 0.80 | 65 | 0VB, IOD |
| 4 | 379 | 0.65 | 0.79 | 46 | 0VB, IOD |
| 5 | 370 | 0.64 | 0.79 | 45 | 0VB, IOD |
Interfaces
3 interfaces between chains.
- A–B · 810 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 795 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 92 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 4FSL · Crystal structure of beta-site app-cleaving enzyme 1 (BACE-DB-MUT) complex with N-(N-(4… · the same entry in another collection · chain E against E, TM-score 1.00
- P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain B 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 4FSL · PDBe 4FSL · UniProt P56817
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