Research workbench
Structure of cathepsin B1 from schistosoma mansoni in complex with WRR286 inhibitor
Analyse Structure of cathepsin B1 from schistosoma mansoni in complex with WRR286… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OGR
- Type
- protein
- Length
- 762 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B-like peptidase (C01 family)
- UniProt
- Q8MNY2
- Ligands
- VS4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cathepsin B-like peptidase (C01 family) | protein | 254 | 27% helix, 23% strand | Q8MNY2 |
Ligands and binding sites
- VS4 · 3-[[N-[4-methyl-piperazinyl]carbonyl]-phenylalaninyl-amino]-5-phenyl-pentane-1-sulfonic acid benzyloxy-amide · ligand · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.76 | 0.79 | 82 | ACT, VS4 |
| 2 | 267 | 0.55 | 0.77 | 33 | VS4 |
| 3 | 223 | 0.53 | 0.77 | 27 | VS4 |
| 4 | 51 | 0.45 | 0.85 | 23 | empty |
| 5 | 63 | 0.34 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 373 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 146 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 covalent (disulfide, covalent ligand).
Compared structures
- 5OGR · Structure of cathepsin B1 from Schistosoma mansoni in complex with WRR286 inhibitor · 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 5OGR · PDBe 5OGR · UniProt Q8MNY2
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