MolNFT v1 · #123117 · protein
Human cathepsin K mutant C25S in complex with the allosteric effector NSC94914
5JA7: “Human cathepsin K mutant C25S in complex with the allosteric effector NSC94914”. X-ray diffraction, 2 ligands (6HM, SO4), 1 pocket (best druggability 0.54). MolNFT v1 #123117 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5JA7
- Type
- protein
- Length
- 445 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
- 6HM, SO4
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin K (EC 3.4.22.38) | protein | 222 | 27% helix, 23% strand | P43235 |
| B | Cathepsin K (EC 3.4.22.38) | protein | 223 | 27% helix, 22% strand | P43235 |
Ligands and binding sites
- 6HM · [([1,1'-biphenyl]-2-yl)methyl]propanedioic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.54 | 0.75 | 34 | 6HM |
Interfaces
1 interface between chains.
- A–B · 87 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5JA7 · Human cathepsin K mutant C25S in complex with the allosteric effector NSC94914 · 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 0.98
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 5JA7 · PDBe 5JA7 · UniProt P43235
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