Research workbench
Structure of potato cathepsin D inhibitor
Analyse Structure of potato cathepsin D inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DZU
- Type
- protein
- Length
- 363 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartic protease inhibitor 11
- UniProt
- P16348
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartic protease inhibitor 11 | protein | 187 | 4% helix, 35% strand | P16348 |
| B | Aspartic protease inhibitor 11 | protein | 176 | 6% helix, 39% strand | P16348 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.59 | 0.75 | 53 | empty |
| 2 | 102 | 0.42 | 0.78 | 24 | empty |
| 3 | 56 | 0.30 | 0.76 | 16 | empty |
| 4 | 50 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 560 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
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 P16348
- Elsewhere: RCSB PDB 5DZU · PDBe 5DZU · UniProt P16348
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