MolNFT v1 · #141384 · protein
Structure of pycnonodysostosis disease related I249T mutant of human cathepsin K
5Z5O: “Structure of pycnonodysostosis disease related I249T mutant of human cathepsin K”. X-ray diffraction, 3 ligands (NA, SO4, CL), 7 pockets (best druggability 0.63). MolNFT v1 #141384 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5Z5O
- Type
- protein
- Length
- 386 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin K
- EC
- 3.4.22.38
- UniProt
- P43235
- Ligands
- NA, SO4, CL
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin K (EC 3.4.22.38) | protein | 309 | 33% helix, 18% strand | P43235 |
| B | Cathepsin K (EC 3.4.22.38) | protein | 77 | 55% helix, 0% strand | P43235 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.63 | 0.83 | 24 | EDO |
| 2 | 108 | 0.55 | 0.84 | 30 | empty |
| 3 | 137 | 0.43 | 0.75 | 18 | EDO |
| 4 | 109 | 0.40 | 0.76 | 20 | GOL |
| 5 | 61 | 0.37 | 0.79 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 5Z5O · Structure of Pycnonodysostosis disease related I249T mutant of human cathepsin K · the same entry in another collection · chain A against A, TM-score 1.00
- P43235 · AlphaFold monomer V2.0 prediction for cathepsin K (P43235) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P43235
- Elsewhere: RCSB PDB 5Z5O · PDBe 5Z5O · UniProt P43235
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