Research workbench
Exploring inhibitor binding at the S subsites of cathepsin L
Analyse Exploring inhibitor binding at the S subsites of cathepsin L in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BC3
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin L heavy and light chains
- EC
- 3.4.22.15
- UniProt
- P07711
- Ligands
- OPT
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin L heavy and light chains (EC 3.4.22.15) | protein | 215 | 30% helix, 22% strand | P07711 |
Ligands and binding sites
- OPT · S-benzyl-N-(biphenyl-4-ylacetyl)-L-cysteinyl-N~5~-(diaminomethyl)-D-ornithyl-N-(2-phenylethyl)-L-tyrosinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.77 | 0.83 | 66 | OPT |
| 2 | 147 | 0.48 | 0.78 | 29 | empty |
| 3 | 68 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 645 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, oxidation).
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 P07711
- Elsewhere: RCSB PDB 3BC3 · PDBe 3BC3 · UniProt P07711
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