Research workbench
Crystal structure of the sphingopyxin I lasso peptide isopeptidase spi-isop (native)
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
- 5JRL
- Type
- protein
- Length
- 2,674 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl AMINOPEPTIDASES/ACYLAMINOACYL-peptidases-like protein
- UniProt
- Q1GQ33
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl AMINOPEPTIDASES/ACYLAMINOACYL-peptidases-like protein | protein | 675 | 22% helix, 35% strand | Q1GQ33 |
| B | Dipeptidyl AMINOPEPTIDASES/ACYLAMINOACYL-peptidases-like protein | protein | 666 | 21% helix, 35% strand | Q1GQ33 |
| C | Dipeptidyl AMINOPEPTIDASES/ACYLAMINOACYL-peptidases-like protein | protein | 664 | 21% helix, 36% strand | Q1GQ33 |
| D | Dipeptidyl AMINOPEPTIDASES/ACYLAMINOACYL-peptidases-like protein | protein | 669 | 22% helix, 36% strand | Q1GQ33 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.77 | 0.83 | 73 | empty |
| 2 | 571 | 0.74 | 0.82 | 51 | empty |
| 3 | 590 | 0.72 | 0.80 | 46 | empty |
| 4 | 409 | 0.72 | 0.83 | 61 | empty |
| 5 | 847 | 0.72 | 0.77 | 63 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2217 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 590 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 510 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 263 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 42 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
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 5JRL · PDBe 5JRL · UniProt Q1GQ33
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