MolNFT v1 · #73529 · protein
Crystal structure of an interleukin-1 receptor complex
3O4O · Interleukin-1 beta: “Crystal structure of an interleukin-1 receptor complex”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability 0.81). MolNFT v1 #73529 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3O4O
- Type
- protein
- Length
- 791 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-1 beta; Interleukin-1 receptor type 2; Interleukin-1 receptor accessory…
- UniProt
- P01584, P27930, Q9NPH3
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 beta | protein | 152 | 4% helix, 45% strand | P01584 |
| C | Interleukin-1 receptor type 2 | protein | 316 | 3% helix, 37% strand | P27930 |
| B | Interleukin-1 receptor accessory protein | protein | 323 | 3% helix, 37% strand | Q9NPH3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.81 | 0.82 | 111 | empty |
| 2 | 192 | 0.74 | 0.90 | 28 | empty |
| 3 | 265 | 0.68 | 0.84 | 34 | empty |
| 4 | 400 | 0.64 | 0.79 | 35 | empty |
| 5 | 127 | 0.63 | 0.86 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2011 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 769 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 597 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3O4O · Crystal structure of an Interleukin-1 receptor complex · the same entry in another collection · chain A against A, TM-score 1.00
- P01584 · AlphaFold monomer V2.0 prediction for interleukin-1 beta (P01584) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q9NPH3 · AlphaFold monomer V2.0 prediction for interleukin-1 receptor accessory protein (Q9NPH3) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P27930 · AlphaFold monomer V2.0 prediction for interleukin-1 receptor type 2 (P27930) · a predicted model of the same protein · chain C against A, TM-score 0.94
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
- Every structure of UniProt P27930
- Every structure of UniProt Q9NPH3
- Elsewhere: RCSB PDB 3O4O · PDBe 3O4O · UniProt P01584 · UniProt P27930 · UniProt Q9NPH3
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