Research workbench
Structure of zymogen of cathepsin B1 from schistosoma mansoni
Analyse Structure of zymogen of cathepsin B1 from schistosoma mansoni in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I04
- Type
- protein
- Length
- 1,228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B-like peptidase (C01 family)
- EC
- 3.4.22.1
- UniProt
- Q8MNY2
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin B-like peptidase (C01 family) (EC 3.4.22.1) | protein | 304 | 29% helix, 23% strand | Q8MNY2 |
| B | Cathepsin B-like peptidase (C01 family) (EC 3.4.22.1) | protein | 310 | 28% helix, 22% strand | Q8MNY2 |
| C | Cathepsin B-like peptidase (C01 family) (EC 3.4.22.1) | protein | 306 | 29% helix, 23% strand | Q8MNY2 |
| D | Cathepsin B-like peptidase (C01 family) (EC 3.4.22.1) | protein | 308 | 26% helix, 22% strand | Q8MNY2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.86 | 0.87 | 122 | EDO |
| 2 | 779 | 0.77 | 0.81 | 78 | empty |
| 3 | 244 | 0.64 | 0.82 | 29 | empty |
| 4 | 70 | 0.44 | 0.82 | 19 | empty |
| 5 | 92 | 0.43 | 0.79 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–D · 940 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 451 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 228 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 117 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 79 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 4I04 · Structure of zymogen of cathepsin B1 from Schistosoma mansoni · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8MNY2
- Elsewhere: RCSB PDB 4I04 · PDBe 4I04 · UniProt Q8MNY2
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