Research workbench
Crystal structure of human il-1BETA in complex with therapeutic antibody binding fragment of gevokizumab
Analyse Crystal structure of human il-1BETA in complex with therapeutic antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G6M
- Type
- protein
- Length
- 583 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-1 beta; Heavy chain of gevokizumab antibody binding fragment; Light chain of…
- UniProt
- P01584
- Pockets
- 10 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-1 beta | protein | 150 | 4% helix, 51% strand | P01584 |
| H | Heavy chain of gevokizumab antibody binding fragment | protein | 220 | 7% helix, 50% strand | — |
| L | Light chain of gevokizumab antibody binding fragment | protein | 213 | 6% helix, 51% strand | — |
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.57 | 0.74 | 41 | empty |
| 2 | 50 | 0.48 | 0.87 | 21 | empty |
| 3 | 174 | 0.45 | 0.74 | 32 | empty |
| 4 | 109 | 0.45 | 0.78 | 21 | empty |
| 5 | 116 | 0.37 | 0.74 | 26 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1819 Ų buried · 11 hydrogen bonds · protein-protein
- A–L · 488 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 477 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4G6M · Crystal structure of human IL-1beta in complex with therapeutic antibody binding fragment… · 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 4G6M · PDBe 4G6M · UniProt P01584
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