Research workbench
The refined 2.15 ångströms X-ray crystal structure of human liver cathepsin B: the structural basis for its specificity
Analyse The refined 2.15 ångströms X-ray crystal structure 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
- 1HUC
- Type
- protein
- Length
- 504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B
- EC
- 3.4.22.1
- UniProt
- P07858
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cathepsin B (EC 3.4.22.1) | protein | 47 | 43% helix, 6% strand | P07858 |
| B, D | Cathepsin B (EC 3.4.22.1) | protein | 205 | 21% helix, 25% strand | P07858 |
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.49 | 0.76 | 29 | empty |
| 2 | 208 | 0.48 | 0.74 | 32 | empty |
| 3 | 138 | 0.38 | 0.73 | 24 | empty |
| 4 | 64 | 0.28 | 0.73 | 16 | empty |
| 5 | 58 | 0.27 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2310 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2288 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1HUC · The refined 2.15 ångströms X-ray crystal structure of human liver cathepsin B: the… · the same entry in another collection · chain D against D, TM-score 1.00
- P07858 · AlphaFold monomer V2.0 prediction for cathepsin B (P07858) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 1HUC · PDBe 1HUC · UniProt P07858
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