MolNFT v1 · #168493 · protein
Crystal structure of human protective PROTEIN/CATHEPSIN a, dfp- inhibited (aged)
6WIA · Lysosomal protective protein: “Crystal structure of human protective PROTEIN/CATHEPSIN a, dfp- inhibited (aged)”. X-ray diffraction, 2 ligands (NAG, CD), 3 pockets (best druggability 0.66). MolNFT v1 #168493 on GenesisL1: 3D…
- PDB
- 6WIA
- Type
- protein
- Length
- 411 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
- NAG, CD
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysosomal protective protein (EC 3.4.16.5) | protein | 411 | 34% helix, 22% strand | P10619 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CD · Cadmium ion · metal · 6 copies · chains A
- ACT · Acetate ion · additive · 5 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.66 | 0.78 | 57 | ACT |
| 2 | 159 | 0.61 | 0.83 | 19 | ACT |
| 3 | 53 | 0.32 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 4 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 6WIA · Crystal structure of human protective PROTEIN/CATHEPSIN a, dfp-inhibited (aged) · the same entry in another collection · chain A against A, TM-score 1.00
- P10619 · AlphaFold monomer V2.0 prediction for lysosomal protective protein (P10619) · a predicted model of the same protein · chain A 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 P10619
- Elsewhere: RCSB PDB 6WIA · PDBe 6WIA · UniProt P10619
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