MolNFT v1 · #88022 · protein
Crystal structure of cathepsin a, complexed with compound 2
4CIB · Lysosomal protective protein: “Crystal structure of cathepsin a, complexed with compound 2”. X-ray diffraction, 3 ligands (7UZ, NAG, CD), 2 pockets (best druggability 0.68). MolNFT v1 #88022 on GenesisL1: 3D structure, binding sites…
- PDB
- 4CIB
- Type
- protein
- Length
- 413 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysosomal protective protein
- EC
- 3.4.16.5
- UniProt
- P10619
- Ligands
- 7UZ, NAG, CD
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysosomal protective protein (EC 3.4.16.5) | protein | 413 | 34% helix, 21% strand | P10619 |
Ligands and binding sites
- 7UZ · 2-(cyclohexylmethyl)propanedioic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CD · Cadmium ion · metal · 5 copies · chains A
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 | 565 | 0.68 | 0.78 | 61 | 7UZ, CD |
| 2 | 84 | 0.41 | 0.78 | 17 | empty |
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 4CIB · PDBe 4CIB · UniProt P10619
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