Research workbench
Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design
Analyse Crystal structures of native and inhibited forms of human cathepsin D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LYB
- Type
- protein
- Length
- 686 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin D; Pepstatin
- EC
- 3.4.23.5
- UniProt
- P07339
- Ligands
- IVA, NAG, BMA, MAN
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cathepsin D (EC 3.4.23.5) | protein | 97 | 7% helix, 55% strand | P07339 |
| B, D | Cathepsin D (EC 3.4.23.5) | protein | 241 | 19% helix, 42% strand | P07339 |
| I, J | Pepstatin | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- IVA · Isovaleric acid · ligand · 2 copies · chains A, B, I, C, D, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.60 | 0.77 | 44 | empty |
| 2 | 247 | 0.54 | 0.76 | 27 | IVA |
| 3 | 258 | 0.52 | 0.75 | 27 | IVA |
| 4 | 56 | 0.27 | 0.74 | 18 | empty |
Interfaces
8 interfaces between chains.
- C–D · 3291 Ų buried · 82 hydrogen bonds · protein-protein
- A–B · 3277 Ų buried · 84 hydrogen bonds · protein-protein
- D–J · 420 Ų buried · 6 hydrogen bonds · protein-protein
- B–I · 397 Ų buried · 9 hydrogen bonds · protein-protein
- C–J · 352 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan, 4 modified, 2 covalent (disulfide, N-glycosylation, nonstandard, covalent ligand).
Compared structures
- 1LYB · Crystal structures of native and inhibited forms of human cathepsin D: implications for… · the same entry in another collection · chain J against J, TM-score 1.00
- P07339 · AlphaFold monomer V2.0 prediction for cathepsin D (P07339) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P07339
- Elsewhere: RCSB PDB 1LYB · PDBe 1LYB · UniProt P07339
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.