Research workbench
Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex: implications for structure- based inhibitor design
Analyse Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CTE
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B
- EC
- 3.4.22.1
- UniProt
- P00787
- Ligands
- PYS
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin B (EC 3.4.22.1) | protein | 253 | 25% helix, 26% strand | P00787 |
Ligands and binding sites
- PYS · 2-pyridinethiol · ligand · 2 copies · chains A, 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 | 929 | 0.77 | 0.80 | 106 | PYS |
Interfaces
1 interface between chains.
- A–B · 803 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1CTE · Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P00787 · AlphaFold monomer V2.0 prediction for cathepsin B (P00787) · 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 P00787
- Elsewhere: RCSB PDB 1CTE · PDBe 1CTE · UniProt P00787
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.