8Z8L | pdb_00008z8l

structure of IL-4Ra in complex with an nanobody 4E9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.96 Å
  • R-Value Free: 
    0.334 (Depositor), 0.335 (DCC) 
  • R-Value Work: 
    0.301 (Depositor), 0.300 (DCC) 
  • R-Value Observed: 
    0.303 (Depositor) 

Starting Model: experimental
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This is version 1.0 of the entry. See complete history


Literature

structure of IL-4Ra in complex with an nanobody 4E9

Song, G.Qiu, W.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-4 receptor subunit alphaA [auth B]214Homo sapiensMutation(s): 1 
Gene Names: IL4RIL4RA582J2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P24394 (Homo sapiens)
Explore P24394 
Go to UniProtKB:  P24394
PHAROS:  P24394
GTEx:  ENSG00000077238 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24394
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P24394-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody dAb1B [auth A]124Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.96 Å
  • R-Value Free:  0.334 (Depositor), 0.335 (DCC) 
  • R-Value Work:  0.301 (Depositor), 0.300 (DCC) 
  • R-Value Observed: 0.303 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.936α = 90
b = 142.936β = 90
c = 149.087γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release