MolNFT v1 · #160610 · protein
Crystal structure of IL17FF bound to Fab fragments of MCAF5352A
6PPG · Interleukin-17F: “Crystal structure of IL17FF bound to Fab fragments of MCAF5352A”. X-ray diffraction, 2 ligands (NAG, CD), 12 pockets (best druggability 0.68). MolNFT v1 #160610 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6PPG
- Type
- protein
- Length
- 1,103 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-17F; Fab MCAF5352A light chain; Fab MCAF5352A heavy chain
- UniProt
- Q96PD4
- Ligands
- NAG, CD
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Interleukin-17F | protein | 109 | 4% helix, 51% strand | Q96PD4 |
| A | Fab MCAF5352A light chain | protein | 212 | 6% helix, 50% strand | — |
| B | Fab MCAF5352A heavy chain | protein | 223 | 7% helix, 49% strand | — |
| H | Fab MCAF5352A heavy chain | protein | 226 | 9% helix, 49% strand | — |
| L | Fab MCAF5352A light chain | protein | 216 | 6% helix, 50% strand | — |
| G | Interleukin-17F | protein | 117 | 3% helix, 52% strand | Q96PD4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains F, G
- CD · Cadmium ion · metal · 53 copies · chains F, H, A, B, G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.68 | 0.82 | 54 | empty |
| 2 | 147 | 0.66 | 0.87 | 29 | CD |
| 3 | 465 | 0.59 | 0.74 | 52 | CD |
| 4 | 444 | 0.58 | 0.74 | 50 | CD |
| 5 | 266 | 0.57 | 0.78 | 34 | empty |
Interfaces
11 interfaces between chains.
- F–G · 3109 Ų buried · 38 hydrogen bonds · protein-protein
- H–L · 1893 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1768 Ų buried · 16 hydrogen bonds · protein-protein
- B–G · 564 Ų buried · 6 hydrogen bonds · protein-protein
- F–H · 475 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
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 Q96PD4
- Elsewhere: RCSB PDB 6PPG · PDBe 6PPG · UniProt Q96PD4
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