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Crystal structure of the sphingopyxin I lasso peptide isopeptidase spi-isop (semet-derived)
Analyse Crystal structure of the sphingopyxin I lasso peptide isopeptidase spi-isop… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JRK
- Type
- protein
- Length
- 1,372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl AMINOPEPTIDASES/ACYLAMINOACYL-peptidases-like protein
- UniProt
- Q1GQ33
- Ligands
- BGC
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl AMINOPEPTIDASES/ACYLAMINOACYL-peptidases-like protein | protein | 695 | 21% helix, 35% strand | Q1GQ33 |
| B | Dipeptidyl AMINOPEPTIDASES/ACYLAMINOACYL-peptidases-like protein | protein | 677 | 21% helix, 35% strand | Q1GQ33 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.78 | 0.82 | 92 | empty |
| 2 | 1104 | 0.76 | 0.79 | 93 | BGC |
| 3 | 434 | 0.71 | 0.82 | 61 | empty |
| 4 | 549 | 0.66 | 0.77 | 38 | empty |
| 5 | 56 | 0.66 | 0.95 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2188 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 5JRK · Crystal Structure of the Sphingopyxin I Lasso Peptide Isopeptidase SpI-IsoP… · 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 Q1GQ33
- Elsewhere: RCSB PDB 5JRK · PDBe 5JRK · UniProt Q1GQ33
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