Research workbench

IL7R in complex with an antagonist

Analyse IL7R in complex with an antagonist in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OPB
Type: protein
Length: 752 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-7 receptor subunit alpha; IL7R binder
UniProt: P16871
Pockets: 1 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Interleukin-7 receptor subunit alpha	protein	196	5% helix, 52% strand	P16871
C	Interleukin-7 receptor subunit alpha	protein	195	5% helix, 52% strand	P16871
D, E, F	IL7R binder	protein	55	84% helix, 0% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, E
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C
PGE · Triethylene glycol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	423	0.66	0.78	38	empty

Interfaces

6 interfaces between chains.

C–F · 776 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 741 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 741 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 139 Å² buried · 1 hydrogen bond · protein-protein
A–B · 84 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

7OPB · IL7R in complex with an antagonist · the same entry in another collection · chain F against F, TM-score 1.00
P16871 · AlphaFold monomer V2.0 prediction for interleukin-7 receptor subunit alpha (P16871) · 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 P16871
Elsewhere: RCSB PDB 7OPB · PDBe 7OPB · UniProt P16871

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