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Trypanosoma brucei procathepsin B solved from 40 fs free-electron laser pulse data by serial femtosecond X-ray crystallography
Analyse Trypanosoma brucei procathepsin B solved from 40 fs free-electron laser pulse… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HWY
- Type
- protein
- Length
- 308 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine peptidase C (cpc)
- EC
- 3.4.22.-
- UniProt
- D6XHE1
- Ligands
- NAG, BMA
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine peptidase C (cpc) (EC 3.4.22.-) | protein | 308 | 28% helix, 24% strand | D6XHE1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.53 | 0.88 | 19 | empty |
| 2 | 143 | 0.53 | 0.81 | 22 | empty |
| 3 | 67 | 0.40 | 0.80 | 20 | empty |
| 4 | 79 | 0.31 | 0.74 | 22 | empty |
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4HWY · Trypanosoma brucei procathepsin B solved from 40 fs free-electron laser pulse data by… · 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 D6XHE1
- Elsewhere: RCSB PDB 4HWY · PDBe 4HWY · UniProt D6XHE1
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