MolNFT v1 · #11546 · protein
Crystal structure of il-17F
1JPY · Interleukin 17F: “Crystal structure of il-17F”. X-ray diffraction, 3 ligands (NAG, NDG, SO4), 8 pockets (best druggability 0.83). MolNFT v1 #11546 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JPY
- Type
- protein
- Length
- 479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin 17F
- Ligands
- NAG, NDG, SO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Interleukin 17F | protein | 121 | 8% helix, 50% strand | — |
| X | Interleukin 17F | protein | 117 | 0% helix, 48% strand | — |
| Y | Interleukin 17F | protein | 120 | 6% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, X, A, Y
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar
- SO4 · Sulfate ion · ion · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.83 | 0.84 | 78 | empty |
| 2 | 168 | 0.53 | 0.79 | 22 | empty |
| 3 | 190 | 0.53 | 0.78 | 25 | empty |
| 4 | 173 | 0.45 | 0.75 | 34 | empty |
| 5 | 69 | 0.42 | 0.80 | 16 | empty |
Interfaces
5 interfaces between chains.
- X–Y · 3534 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3486 Ų buried · 48 hydrogen bonds · protein-protein
- B–X · 610 Ų buried · 4 hydrogen bonds · protein-protein
- B–Y · 183 Ų buried · 1 hydrogen bond · protein-protein
- A–X · 174 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1JPY · Crystal structure of IL-17F · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1JPY · PDBe 1JPY
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