MolNFT v1 · #126520 · protein
Crystal structure of a interleukin-2 variant in complex with interleukin-2 receptor
5M5E · Interleukin-2 receptor subunit beta: “Crystal structure of a interleukin-2 variant in complex with interleukin-2 receptor”. X-ray diffraction, 5 ligands (CYS, NAG, FUC), 7 pockets (best druggability 0.56). MolNFT v1 #126520 on…
- PDB
- 5M5E
- Type
- protein
- Length
- 517 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-2 receptor subunit beta; Cytokine receptor common subunit gamma; Interleukin-2
- UniProt
- P14784, P31785
- Ligands
- CYS, NAG, FUC, MAN, SO4
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Interleukin-2 receptor subunit beta | protein | 203 | 3% helix, 47% strand | P14784 |
| C | Cytokine receptor common subunit gamma | protein | 193 | 5% helix, 46% strand | P31785 |
| D | Interleukin-2 | protein | 121 | 64% helix, 3% strand | — |
Ligands and binding sites
- CYS · Cysteine · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains B, C
- MAN · alpha-D-mannopyranose · sugar · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.56 | 0.78 | 30 | empty |
| 2 | 91 | 0.47 | 0.81 | 14 | empty |
| 3 | 152 | 0.47 | 0.77 | 36 | empty |
| 4 | 111 | 0.43 | 0.78 | 21 | empty |
| 5 | 163 | 0.41 | 0.73 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–C · 992 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 735 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 536 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 7 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand, C-mannosylation).
Compared structures
- 5M5E · Crystal structure of a interleukin-2 variant in complex with interleukin-2 receptor · the same entry in another collection · chain B against B, TM-score 1.00
- 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 0.99
- 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
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 P14784
- Every structure of UniProt P31785
- Elsewhere: RCSB PDB 5M5E · PDBe 5M5E · UniProt P14784 · UniProt P31785
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