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Crystal structure of the tetragonal form of human liver cathepsin B
Analyse Crystal structure of the tetragonal form of human liver cathepsin B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IPP
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B
- EC
- 3.4.22.1
- UniProt
- P07858
- Ligands
- PYS
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin B (EC 3.4.22.1) | protein | 47 | 53% helix, 9% strand | P07858 |
| B | Cathepsin B | protein | 205 | 21% helix, 26% strand | P07858 |
Ligands and binding sites
- PYS · 2-pyridinethiol · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.48 | 0.76 | 36 | PYS |
| 2 | 75 | 0.36 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2332 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 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 P07858
- Elsewhere: RCSB PDB 2IPP · PDBe 2IPP · UniProt P07858
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