Research workbench
Crystal structure of BACE1 with its inhibitor
Analyse Crystal structure of BACE1 with its inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UQR
- Type
- protein
- Length
- 1,143 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1; Methyl (2S)-1-[(2R,5S,8S,12S,13S)-2,13-dibenzyl-12-hydroxy…
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- QSC, ZSC
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 14% helix, 39% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 374 | 15% helix, 40% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 12% helix, 39% strand | P56817 |
| D, E, F | Methyl (2S)-1-[(2R,5S,8S,12S,13S)-2,13-dibenzyl-12-hydroxy- 3,5-dimethyl-15-(3-[METHYL(METHYLSULFONYL)AMINO]-5-{[(1R)-1- PHENYLETHYL]CARBAMOYL}PHENYL)-8-(2-methylpropyl)-4,7,10,15-tetraoxo- 3,6,9,14-tetraazapentadecan-1-OYL]PYRROLIDINE-2-carboxylate | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- QSC · (1R)-1-phenylethanamine · ligand · 3 copies · chains A, D, B, E, C, F
- ZSC · 5-[methyl(methylsulfonyl)amino]benzene-1,3-dicarboxylic acid · ligand · 3 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.73 | 0.76 | 90 | empty |
| 2 | 253 | 0.63 | 0.81 | 43 | QSC, ZSC |
| 3 | 159 | 0.59 | 0.83 | 33 | QSC, ZSC |
| 4 | 191 | 0.54 | 0.79 | 33 | QSC, ZSC |
| 5 | 75 | 0.47 | 0.82 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–D · 603 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 580 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 571 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 548 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 364 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 9 modified, 3 covalent (disulfide, nonstandard, covalent ligand).
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 3UQR · PDBe 3UQR · UniProt P56817
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