Research workbench
Cathepsin B in complex with darpin 81
Analyse Cathepsin B in complex with darpin 81 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MBL
- Type
- protein
- Length
- 420 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B; Darpin 81
- EC
- 3.4.22.1
- UniProt
- P07858
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin B (EC 3.4.22.1) | protein | 255 | 27% helix, 25% strand | P07858 |
| B | Darpin 81 | protein | 165 | 52% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.66 | 0.78 | 44 | empty |
| 2 | 101 | 0.62 | 0.88 | 37 | empty |
| 3 | 235 | 0.53 | 0.77 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 964 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 modified (disulfide, methylation).
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 5MBL · PDBe 5MBL · UniProt P07858
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