Research workbench
Cytokine receptor complex - crystal form 1A
Analyse Cytokine receptor complex - crystal form 1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NN5
- Type
- protein
- Length
- 489 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymic stromal lymphopoietin; Interleukin-7 receptor subunit alpha; Cytokine…
- UniProt
- Q9JIE6, P16872, Q8CII9
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymic stromal lymphopoietin | protein | 109 | 66% helix, 2% strand | Q9JIE6 |
| B | Interleukin-7 receptor subunit alpha | protein | 197 | 5% helix, 51% strand | P16872 |
| C | Cytokine receptor-like factor 2 | protein | 183 | 6% helix, 47% strand | Q8CII9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- ACT · Acetate ion · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.58 | 0.75 | 37 | empty |
| 2 | 400 | 0.56 | 0.74 | 39 | empty |
| 3 | 65 | 0.50 | 0.85 | 24 | empty |
| 4 | 60 | 0.30 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 710 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 654 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 110 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4NN5 · Cytokine receptor complex - Crystal form 1A · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JIE6 · AlphaFold monomer V2.0 prediction for thymic stromal lymphopoietin (Q9JIE6) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P16872 · AlphaFold monomer V2.0 prediction for interleukin-7 receptor subunit alpha (P16872) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q8CII9 · AlphaFold monomer V2.0 prediction for cytokine receptor-like factor 2 (Q8CII9) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q9JIE6
- Every structure of UniProt P16872
- Every structure of UniProt Q8CII9
- Elsewhere: RCSB PDB 4NN5 · PDBe 4NN5 · UniProt Q9JIE6 · UniProt P16872 · UniProt Q8CII9
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