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The structure of il-13 in complex with il-13RALPHA2

Analyse The structure of il-13 in complex with il-13RALPHA2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LB6
Type: protein
Length: 756 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-13; Interleukin-13 receptor subunit alpha-2
UniProt: P35225, A8K7E2
Ligands: NAG, CA
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Interleukin-13	protein	109	50% helix, 7% strand	P35225
C	Interleukin-13 receptor subunit alpha-2	protein	252	3% helix, 44% strand	A8K7E2
D	Interleukin-13 receptor subunit alpha-2	protein	286	2% helix, 47% strand	A8K7E2

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, D
CA · Calcium ion · metal · 2 copies · chains C, B, D

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	737	0.69	0.76	75	CA
2	551	0.63	0.75	53	CA
3	63	0.36	0.78	14	empty
4	122	0.35	0.73	21	empty
5	60	0.33	0.77	15	empty

Interfaces

4 interfaces between chains.

B–D · 969 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 939 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 192 Å² buried · 1 hydrogen bond · protein-protein
C–D · 54 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 13 disulfide, 5 modified, 2 glycan (disulfide, methylation, N-glycosylation).

Compared structures

3LB6 · The structure of IL-13 in complex with IL-13Ralpha2 · the same entry in another collection · chain A against A, TM-score 1.00
P35225 · AlphaFold monomer V2.0 prediction for interleukin-13 (P35225) · a predicted model of the same protein · chain A 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 P35225
Every structure of UniProt A8K7E2
Elsewhere: RCSB PDB 3LB6 · PDBe 3LB6 · UniProt P35225 · UniProt A8K7E2

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