Research workbench
Co-complex of S. pyogenes 10782 streptopain bound with a sufex-based optimized small molecule inhibitor
Analyse Co-complex of S. pyogenes 10782 streptopain bound with a sufex-based optimized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UQD
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptopain
- EC
- 3.4.22.10
- UniProt
- P0C0J0
- Ligands
- QF4
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptopain (EC 3.4.22.10) | protein | 247 | 26% helix, 22% strand | P0C0J0 |
| B | Streptopain (EC 3.4.22.10) | protein | 254 | 28% helix, 22% strand | P0C0J0 |
Ligands and binding sites
- QF4 · Benzyl [(1S)-2-(3-{[(4-carbamoylpiperidin-1-yl) (fluoro)oxo-lambda~6~-sulfanylidene]amino}phenyl)-1-cyanoethyl]carbamate · ligand · 2 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 | 155 | 0.48 | 0.78 | 19 | empty |
| 2 | 124 | 0.46 | 0.78 | 19 | empty |
| 3 | 73 | 0.35 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 621 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6UQD · Co-complex of S. pyogenes 10782 streptopain bound with a SuFEx-based optimized small… · the same entry in another collection · chain A against A, TM-score 1.00
- P0C0J0 · AlphaFold monomer V2.0 prediction for streptopain (P0C0J0) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P0C0J0
- Elsewhere: RCSB PDB 6UQD · PDBe 6UQD · UniProt P0C0J0
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