MolNFT v1 · #28637 · protein

Crystal structure of insect cell expressed il-22

1YKB · Protein (interleukin-22): “Crystal structure of insect cell expressed il-22”. X-ray diffraction, 3 ligands (NAG, FUC, MAN), 16 pockets (best druggability 0.60). MolNFT v1 #28637 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1YKB
Type: protein
Length: 851 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (interleukin-22)
UniProt: Q9GZX6
Ligands: NAG, FUC, MAN
Pockets: 16 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein (interleukin-22)	protein	141	72% helix, 0% strand	Q9GZX6
B, C, D, E, F	Protein (interleukin-22)	protein	142	65% helix, 0% strand	Q9GZX6

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, D, E, F
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, D
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	223	0.60	0.81	26	empty
2	211	0.59	0.80	26	empty
3	182	0.59	0.82	31	empty
4	281	0.56	0.77	25	empty
5	139	0.56	0.82	24	empty

Interfaces

6 interfaces between chains.

C–D · 1109 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1095 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1091 Å² buried · 9 hydrogen bonds · protein-protein
A–F · 497 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 486 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 9 glycan (disulfide, N-glycosylation).

Compared structures

1YKB · Crystal Structure of Insect Cell Expressed IL-22 · the same entry in another collection · chain F against F, TM-score 1.00
Q9GZX6 · AlphaFold monomer V2.0 prediction for interleukin-22 (Q9GZX6) · a predicted model of the same protein · chain A 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
Elsewhere: RCSB PDB 1YKB · PDBe 1YKB · UniProt Q9GZX6

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