Research workbench
Structure of a 60 nm small molecule bound to a hot spot on il-2
Analyse Structure of a 60 nm small molecule bound to a hot spot on il-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PY2
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-2
- UniProt
- P60568
- Ligands
- FRH, ZN
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-2 | protein | 117 | 68% helix, 3% strand | P60568 |
| B | Interleukin-2 | protein | 116 | 71% helix, 3% strand | P60568 |
| C | Interleukin-2 | protein | 115 | 59% helix, 3% strand | P60568 |
| D | Interleukin-2 | protein | 120 | 70% helix, 3% strand | P60568 |
Ligands and binding sites
- FRH · 5-[2,3-dichloro-4-(5-{1-[2-(2-guanidino-4-methyl-pentanoylamino)-acetyl]-piperidin-4-yl}-1-methyl-1H-pyrazol-3-yl)-phenoxymethyl]-furan-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.35 | 0.74 | 14 | empty |
| 2 | 52 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- B–C · 142 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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
- Elsewhere: RCSB PDB 1PY2 · PDBe 1PY2 · UniProt P60568
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