Research workbench
Structure of a cytokine receptor complex
Analyse Structure of a cytokine receptor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NKQ
- Type
- protein
- Length
- 708 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytokine receptor common subunit beta; Granulocyte-macrophage colony-stimulating factor…
- UniProt
- P32927, P04141, P15509
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokine receptor common subunit beta | protein | 412 | 5% helix, 42% strand | P32927 |
| C | Granulocyte-macrophage colony-stimulating factor | protein | 105 | 53% helix, 6% strand | P04141 |
| B | Granulocyte-macrophage colony-stimulating factor receptor subunit alpha | protein | 191 | 2% helix, 23% strand | P15509 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.72 | 0.84 | 44 | empty |
| 2 | 466 | 0.65 | 0.78 | 53 | empty |
| 3 | 195 | 0.64 | 0.84 | 35 | empty |
| 4 | 235 | 0.60 | 0.80 | 28 | empty |
| 5 | 303 | 0.57 | 0.76 | 43 | empty |
Interfaces
3 interfaces between chains.
- C–B · 610 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 554 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 382 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 4NKQ · Structure of a Cytokine Receptor Complex · the same entry in another collection · chain A against A, TM-score 1.00
- P04141 · AlphaFold monomer V2.0 prediction for granulocyte-macrophage colony- stimulating factor… · a predicted model of the same protein · chain C against A, TM-score 0.95
- P15509 · AlphaFold monomer V2.0 prediction for granulocyte-macrophage colony- stimulating factor… · a predicted model of the same protein · chain B against A, TM-score 0.93
- P32927 · AlphaFold monomer V2.0 prediction for cytokine receptor common subunit beta (P32927) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P32927
- Every structure of UniProt P04141
- Every structure of UniProt P15509
- Elsewhere: RCSB PDB 4NKQ · PDBe 4NKQ · UniProt P32927 · UniProt P04141 · UniProt P15509
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.