9EZA | pdb_00009eza

Interleukin-31 Receptor D1D2 in complex with Nemolizumab derived scFv

• PDB DOI: https://doi.org/10.2210/pdb9EZA/pdb

• Classification: CYTOKINE
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2024-04-11 Released: 2025-07-16 
• Deposition Author(s): Bloch, Y., Savvides, S.N.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.201 (DCC) 

Starting Model: experimental

Literature

Structural basis of the Interleukin-31 signaling complex and its inhibition.

Bloch, Y., Savvides, S.N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 117.38 kDa 
• Atom Count: 7,222 
• Modeled Residue Count: 876 
• Deposited Residue Count: 1,042 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nemolizumab scFv	A, C	260	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-31 receptor subunit alpha	B, D	261	Homo sapiens	Mutation(s): 0  Gene Names: IL31RA, CRL3, GPL, UNQ6368/PRO21073/PRO21384
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NI17 (Homo sapiens) Explore Q8NI17  Go to UniProtKB:  Q8NI17
PHAROS:  Q8NI17 GTEx:  ENSG00000164509
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q8NI17-1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth B], G [auth B], H [auth D], I [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
A1H79	J [auth D]	BES buffer C6 H15 N O5 S AJTVSSFTXWNIRG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.201 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.008	α = 90
b = 163.559	β = 90
c = 269.466	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Bloch, Y., Savvides, S.N.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	12S0519N

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release