MolNFT v1 · #59890 · protein
Chagasin-cathepsin B complex
3CBJ: “Chagasin-cathepsin B complex”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.37). MolNFT v1 #59890 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3CBJ
- Type
- protein
- Length
- 367 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B; Chagasin
- EC
- 3.4.22.1
- UniProt
- P07858, Q966X9
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin B (EC 3.4.22.1) | protein | 258 | 26% helix, 22% strand | P07858 |
| B | Chagasin | protein | 109 | 6% helix, 50% strand | Q966X9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.37 | 0.78 | 20 | empty |
| 2 | 74 | 0.36 | 0.77 | 21 | empty |
| 3 | 58 | 0.26 | 0.73 | 17 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1221 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3CBJ · Chagasin-Cathepsin B complex · the same entry in another collection · chain A against A, 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
- Q966X9 · AlphaFold monomer V2.0 prediction for chagasin (Q966X9) · a predicted model of the same protein · chain B against A, TM-score 0.96
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
- Every structure of UniProt Q966X9
- Elsewhere: RCSB PDB 3CBJ · PDBe 3CBJ · UniProt P07858 · UniProt Q966X9
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