Research workbench
Crystal structure of human beta secretase in complex with nvp-BUR436, derived from a co-crystallization experiment
Analyse Crystal structure of human beta secretase in complex with nvp-BUR436, derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D83
- Type
- protein
- Length
- 1,131 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
- 0GT
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 14% helix, 41% strand | P56817 |
Ligands and binding sites
- 0GT · (3R,4S,5S)-3-[(3-tert-butylbenzyl)amino]-5-{[3-(2,2-difluoroethyl)-1H-indol-5-yl]methyl}tetrahydro-2H-thiopyran-4-ol 1,1-dioxide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.75 | 0.78 | 97 | 0GT |
| 2 | 414 | 0.67 | 0.80 | 45 | 0GT |
| 3 | 398 | 0.67 | 0.80 | 42 | 0GT |
| 4 | 170 | 0.58 | 0.82 | 36 | empty |
| 5 | 134 | 0.55 | 0.82 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1058 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 560 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4D83 · Crystal Structure of Human Beta Secretase in Complex with NVP-BUR436, derived from a… · the same entry in another collection · chain A against A, 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 0.99
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 4D83 · PDBe 4D83 · UniProt P56817
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