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Crystal structure of the IL4-IL4R-IL13RA ternary complex

Analyse Crystal structure of the IL4-IL4R-IL13RA ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BPN
Type: protein
Length: 620 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-4; Interleukin-4 receptor alpha chain; Interleukin-13 receptor alpha-1 chain
UniProt: P05112, P24394, P78552
Ligands: NAG
Pockets: 8 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interleukin-4	protein	126	65% helix, 5% strand	P05112
B	Interleukin-4 receptor alpha chain	protein	199	7% helix, 48% strand	P24394
C	Interleukin-13 receptor alpha-1 chain	protein	295	2% helix, 46% strand	P78552

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	398	0.66	0.80	46	empty
2	364	0.61	0.77	61	empty
3	125	0.60	0.86	29	empty
4	403	0.59	0.75	48	empty
5	227	0.54	0.77	29	empty

Interfaces

3 interfaces between chains.

A–C · 932 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 736 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 714 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

3BPN · Crystal structure of the IL4-IL4R-IL13Ra ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
P78552 · AlphaFold monomer V2.0 prediction for interleukin-13 receptor subunit alpha-1 (P78552) · a predicted model of the same protein · chain C against A, TM-score 0.98
P05112 · AlphaFold monomer V2.0 prediction for interleukin-4 (P05112) · a predicted model of the same protein · chain A against A, TM-score 0.96
P24394 · AlphaFold monomer V2.0 prediction for interleukin-4 receptor subunit alpha (P24394) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P05112
Every structure of UniProt P24394
Every structure of UniProt P78552
Elsewhere: RCSB PDB 3BPN · PDBe 3BPN · UniProt P05112 · UniProt P24394 · UniProt P78552

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