MolNFT v1 · #61261 · protein

Structure of il-22/IL-22R1

3DGC · Interleukin-22: “Structure of il-22/IL-22R1”. X-ray diffraction, 7 ligands (IUM, NAG, BMA), 7 pockets (best druggability 0.65). MolNFT v1 #61261 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3DGC
Type: protein
Length: 691 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-22; Interleukin-22 receptor subunit alpha-1
UniProt: Q9GZX6, Q9HB22
Ligands: IUM, NAG, BMA, MAN, FUC, U1, CL
Pockets: 7 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	Interleukin-22	protein	141	71% helix, 0% strand	Q9GZX6
R	Interleukin-22 receptor subunit alpha-1	protein	202	5% helix, 51% strand	Q9HB22
S	Interleukin-22 receptor subunit alpha-1	protein	207	7% helix, 48% strand	Q9HB22

Ligands and binding sites

IUM · Uranyl (VI) ion · ligand · chains M
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains R, M
BMA · beta-D-mannopyranose · sugar
MAN · alpha-D-mannopyranose · sugar · chains M
FUC · alpha-L-fucopyranose · sugar · chains R, M
U1 · Uranium atom · metal · 11 copies · chains L, R, M, S
CL · Chloride ion · ion · 3 copies · chains R, S
ACT · Acetate ion · additive · 2 copies · chains M

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	286	0.65	0.81	32	empty
2	325	0.65	0.80	29	empty
3	52	0.53	0.89	14	empty
4	111	0.53	0.82	20	empty
5	268	0.52	0.74	42	empty

Interfaces

4 interfaces between chains.

L–R · 858 Å² buried · 17 hydrogen bonds · protein-protein
M–S · 853 Å² buried · 16 hydrogen bonds · protein-protein
R–M · 610 Å² buried · 8 hydrogen bonds · protein-protein
L–S · 580 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

3DGC · Structure of IL-22/IL-22R1 · the same entry in another collection · chain L against L, TM-score 1.00
Q9GZX6 · AlphaFold monomer V2.0 prediction for interleukin-22 (Q9GZX6) · a predicted model of the same protein · chain L against A, TM-score 0.99

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 Q9GZX6
Every structure of UniProt Q9HB22
Elsewhere: RCSB PDB 3DGC · PDBe 3DGC · UniProt Q9GZX6 · UniProt Q9HB22

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