Research workbench
Mouse cathepsin S with covalent ligand
Analyse Mouse cathepsin S with covalent ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BPV
- Type
- protein
- Length
- 1,184 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin S
- EC
- 3.4.22.27
- UniProt
- O70370
- Ligands
- OFH
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cathepsin S (EC 3.4.22.27) | protein | 219 | 27% helix, 23% strand | O70370 |
| K | Cathepsin S (EC 3.4.22.27) | protein | 89 | 17% helix, 30% strand | O70370 |
Ligands and binding sites
- OFH · (4R)-4-[(2-chloro-4-{[(2S)-1,1,1-trifluoropropan-2-yl]oxy}phenyl)sulfonyl]-N-{1-[(E)-iminomethyl]cyclopropyl}-1-{[1-(trifluoromethyl)cyclopropyl]carbonyl}-L-prolinamide · ligand · 5 copies · chains A, D, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.83 | 0.84 | 120 | OFH |
| 2 | 432 | 0.70 | 0.81 | 67 | empty |
| 3 | 608 | 0.65 | 0.75 | 52 | empty |
| 4 | 292 | 0.59 | 0.78 | 33 | empty |
| 5 | 102 | 0.43 | 0.78 | 19 | OFH |
Interfaces
9 interfaces between chains.
- A–C · 634 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 446 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 388 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 384 Ų buried · 6 hydrogen bonds · protein-protein
- D–K · 344 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 5 covalent (disulfide, covalent ligand).
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 O70370
- Elsewhere: RCSB PDB 4BPV · PDBe 4BPV · UniProt O70370
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