MolNFT v1 · #146395 · protein
Structure of a de novo designed interleukin-2/INTERLEUKIN-15 mimetic complex with il-2RB and il-2RG
6DG5 · Neoleukin-2/15: “Structure of a de novo designed interleukin-2/INTERLEUKIN-15 mimetic complex with il-2RB and il-2RG”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 5 pockets (best druggability 0.59). MolNFT v1 #146395 on GenesisL1…
- PDB
- 6DG5
- Type
- protein
- Length
- 492 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neoleukin-2/15; Interleukin-2 receptor subunit beta; Cytokine receptor common subunit…
- UniProt
- P16297, P34902
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neoleukin-2/15 | protein | 93 | 86% helix, 0% strand | — |
| B | Interleukin-2 receptor subunit beta | protein | 206 | 3% helix, 48% strand | P16297 |
| C | Cytokine receptor common subunit gamma | protein | 193 | 5% helix, 44% strand | P34902 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.59 | 0.86 | 21 | NAG |
| 2 | 82 | 0.47 | 0.82 | 22 | empty |
| 3 | 152 | 0.45 | 0.76 | 19 | empty |
| 4 | 111 | 0.37 | 0.74 | 16 | empty |
| 5 | 58 | 0.34 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 883 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 734 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 591 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6DG5 · Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic complex with IL-2Rb… · the same entry in another collection · chain A against A, TM-score 1.00
- P16297 · AlphaFold monomer V2.0 prediction for interleukin-2 receptor subunit beta (P16297) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P34902 · AlphaFold monomer V2.0 prediction for cytokine receptor common subunit gamma (P34902) · 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 P16297
- Every structure of UniProt P34902
- Elsewhere: RCSB PDB 6DG5 · PDBe 6DG5 · UniProt P16297 · UniProt P34902
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