Research workbench
Crystal structure of cathepsin B from trypanosoma brucei
Analyse Crystal structure of cathepsin B from trypanosoma brucei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MOR
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B-like cysteine protease
- EC
- 3.4.22.-
- UniProt
- Q6R7Z5
- Ligands
- NAG, NA, CL
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin B-like cysteine protease (EC 3.4.22.-) | protein | 260 | 23% helix, 25% strand | Q6R7Z5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.55 | 0.80 | 26 | GOL |
| 2 | 168 | 0.54 | 0.80 | 27 | GOL |
| 3 | 126 | 0.38 | 0.73 | 19 | GOL |
| 4 | 113 | 0.37 | 0.74 | 18 | empty |
| 5 | 69 | 0.28 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 737 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3MOR · Crystal structure of Cathepsin B from Trypanosoma Brucei · 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 Q6R7Z5
- Elsewhere: RCSB PDB 3MOR · PDBe 3MOR · UniProt Q6R7Z5
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