MolNFT v1 · #91947 · protein
Crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with N-(N-(4-amino-3,5- DICHLOROBENZYL)CARBAMIMIDOYL)-3-(4- methoxyphenyl)-5- methyl-4-isothiazolecarboxamide
4FSE · Beta-secretase 1: “Crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with N-(N-(4-amino-3,5…”. X-ray diffraction, 2 ligands (0VA, IOD), 16 pockets (best druggability 0.73). MolNFT v1 #91947 on GenesisL1: 3D…
- PDB
- 4FSE
- 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
- 0VA, IOD
- Pockets
- 16 · 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
- 0VA · N-[N-(4-amino-3,5-dichlorobenzyl)carbamimidoyl]-3-(4-methoxyphenyl)-5-methyl-1,2-thiazole-4-carboxamide · ligand · 4 copies · chains A, B, D, E
- IOD · Iodide ion · ion · 9 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.73 | 0.84 | 33 | empty |
| 2 | 401 | 0.72 | 0.83 | 32 | empty |
| 3 | 382 | 0.64 | 0.79 | 46 | 0VA, IOD |
| 4 | 410 | 0.64 | 0.78 | 49 | 0VA, IOD |
| 5 | 399 | 0.64 | 0.78 | 50 | 0VA, IOD |
Interfaces
3 interfaces between chains.
- D–E · 770 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 763 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 93 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4FSE · crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with… · 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 4FSE · PDBe 4FSE · UniProt P56817
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