Research workbench
Crystal structure of cathepsin a, complexed with 8A.
Analyse Crystal structure of cathepsin a, complexed with 8A. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AZ0
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysosomal protective protein 32 kda chain; Lysosomal protective protein 20 kda chain
- EC
- 3.4.16.5
- UniProt
- P10619
- Ligands
- S61, NAG, CD
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysosomal protective protein 32 kda chain (EC 3.4.16.5) | protein | 260 | 32% helix, 21% strand | P10619 |
| B | Lysosomal protective protein 20 kda chain (EC 3.4.16.5) | protein | 153 | 35% helix, 22% strand | P10619 |
Ligands and binding sites
- S61 · (S)-3-{[1-(2-Fluoro-phenyl)-5-hydroxy-1H-pyrazole-3-carbonyl]-amino}-3-o-tolyl-propionic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CD · Cadmium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.68 | 0.78 | 62 | S61, CD |
| 2 | 55 | 0.33 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4060 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 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 P10619
- Elsewhere: RCSB PDB 4AZ0 · PDBe 4AZ0 · UniProt P10619
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