MolNFT v1 · #151208 · protein

Crystal structure of human il-17F

6HGO · Interleukin-17F: “Crystal structure of human il-17F”. X-ray diffraction, 2 ligands (NAG, SO4), 14 pockets (best druggability 0.85). MolNFT v1 #151208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6HGO
Type: protein
Length: 496 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-17F
UniProt: Q96PD4
Ligands: NAG, SO4
Pockets: 14 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interleukin-17F	protein	126	6% helix, 48% strand	Q96PD4
B	Interleukin-17F	protein	122	8% helix, 46% strand	Q96PD4
C	Interleukin-17F	protein	127	8% helix, 45% strand	Q96PD4
D	Interleukin-17F	protein	121	8% helix, 46% strand	Q96PD4

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A, C, D
SO4 · Sulfate ion · ion · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	980	0.85	0.86	71	empty
2	203	0.58	0.80	23	empty
3	166	0.50	0.78	25	empty
4	78	0.45	0.81	18	empty
5	111	0.43	0.77	16	empty

Interfaces

5 interfaces between chains.

C–D · 3663 Å² buried · 52 hydrogen bonds · protein-protein
A–B · 3553 Å² buried · 54 hydrogen bonds · protein-protein
B–D · 653 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 260 Å² buried · 1 hydrogen bond · protein-protein
A–D · 126 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6HGO · Crystal Structure of human IL-17F · the same entry in another collection · chain D against D, TM-score 1.00
Q96PD4 · AlphaFold monomer V2.0 prediction for interleukin-17F (Q96PD4) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 6HGO · PDBe 6HGO · UniProt Q96PD4

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