MolNFT v1 · #92390 · protein
Crystal structure of human il-1BETA in complex with the therapeutic antibody binding fragment of canakinumab
4G6J · Interleukin-1 beta: “Crystal structure of human il-1BETA in complex with the therapeutic antibody binding fragment of canakinumab”. X-ray diffraction, 7 pockets (best druggability 0.67). MolNFT v1 #92390 on GenesisL1: 3D structure…
- PDB
- 4G6J
- Type
- protein
- Length
- 579 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-1 beta; Heavy chain of antibody binding fragment of canakinumab; Light chain…
- UniProt
- P01584
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 beta | protein | 149 | 6% helix, 49% strand | P01584 |
| H | Heavy chain of antibody binding fragment of canakinumab | protein | 218 | 8% helix, 51% strand | — |
| L | Light chain of antibody binding fragment of canakinumab | protein | 212 | 7% helix, 50% strand | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.67 | 0.76 | 68 | empty |
| 2 | 50 | 0.52 | 0.89 | 20 | empty |
| 3 | 112 | 0.45 | 0.79 | 21 | empty |
| 4 | 81 | 0.36 | 0.76 | 18 | empty |
| 5 | 71 | 0.31 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1920 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 744 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 377 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4G6J · Crystal structure of human IL-1beta in complex with the therapeutic antibody binding… · 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 0.98
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 4G6J · PDBe 4G6J · UniProt P01584
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