Research workbench
IL-1beta in complex with macrocyclic peptide hit
Analyse IL-1beta in complex with macrocyclic peptide hit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8RYK
- Type
- protein
- Length
- 336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Interleukin-1 beta; Macrocyclic peptide
- UniProt
- P01584
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.8 · 3 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Interleukin-1 beta | protein | 153 | 6% helix, 48% strand | P01584 |
| C | Macrocyclic peptide | protein | 14 | 0% helix, 21% strand | — |
| D | Macrocyclic peptide | protein | 16 | 0% helix, 19% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.63 | 0.79 | 46 | empty |
| 2 | 52 | 0.34 | 0.78 | 16 | empty |
| 3 | 56 | 0.27 | 0.73 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–D · 727 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 719 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 593 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 243 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- P01584 · AlphaFold monomer V2.0 prediction for interleukin-1 beta (P01584) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P01584
- Elsewhere: RCSB PDB 8RYK · PDBe 8RYK · UniProt P01584
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