MolNFT v1 · #31768 · protein
Cytokine receptor complex
2B5I · Interleukin-2: “Cytokine receptor complex”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.61). MolNFT v1 #31768 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2B5I
- Type
- protein
- Length
- 629 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-2; Interleukin-2 receptor beta chain; Cytokine receptor common gamma chain…
- UniProt
- P60568, P14784, P31785, P01589
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-2 | protein | 120 | 64% helix, 3% strand | P60568 |
| B | Interleukin-2 receptor beta chain | protein | 196 | 3% helix, 46% strand | P14784 |
| C | Cytokine receptor common gamma chain | protein | 191 | 3% helix, 46% strand | P31785 |
| D | Interleukin-2 receptor alpha chain | protein | 122 | 0% helix, 37% strand | P01589 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.61 | 0.79 | 32 | empty |
| 2 | 140 | 0.57 | 0.83 | 20 | empty |
| 3 | 66 | 0.44 | 0.82 | 20 | empty |
| 4 | 99 | 0.43 | 0.78 | 15 | empty |
| 5 | 122 | 0.42 | 0.76 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 948 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 891 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 695 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 537 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2B5I · cytokine receptor complex · the same entry in another collection · chain D against D, TM-score 1.00
- P14784 · AlphaFold monomer V2.0 prediction for interleukin-2 receptor subunit beta (P14784) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P31785 · AlphaFold monomer V2.0 prediction for cytokine receptor common subunit gamma (P31785) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P60568 · AlphaFold monomer V2.0 prediction for interleukin-2 (P60568) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P01589 · AlphaFold monomer V2.0 prediction for interleukin-2 receptor subunit alpha (P01589) · a predicted model of the same protein · chain D 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 P60568
- Every structure of UniProt P14784
- Every structure of UniProt P31785
- Every structure of UniProt P01589
- Elsewhere: RCSB PDB 2B5I · PDBe 2B5I · UniProt P60568 · UniProt P14784 · UniProt P31785 · UniProt P01589
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