3QWR

Crystal structure of IL-23 in complex with an adnectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report



Literature

Structures of adnectin/protein complexes reveal an expanded binding footprint.

Ramamurthy, V.Krystek, S.R.Bush, A.Wei, A.Emanuel, S.L.Das Gupta, R.Janjua, A.Cheng, L.Murdock, M.Abramczyk, B.Cohen, D.Lin, Z.Morin, P.Davis, J.H.Dabritz, M.McLaughlin, D.C.Russo, K.A.Chao, G.Wright, M.C.Jenny, V.A.Engle, L.J.Furfine, E.Sheriff, S.

(2012) Structure 20: 259-269

  • DOI: 10.1016/j.str.2011.11.016
  • Primary Citation of Related Structures:  
    3QWQ, 3QWR

  • PubMed Abstract: 
  • Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin (¹⁰Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three ¹⁰Fn3 loops that ...

    Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin (¹⁰Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three ¹⁰Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the β strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these β strand interactions, indicating that these nonloop residues can expand the available binding footprint.


    Organizational Affiliation

    Bristol-Myers Squibb Research & Development, Princeton, NJ 08543-4000, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-12 subunit betaA306Homo sapiensMutation(s): 0 
Gene Names: IL12BNKSF2
Find proteins for P29460 (Homo sapiens)
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Go to UniProtKB:  P29460
NIH Common Fund Data Resources
PHAROS  P29460
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-23 subunit alphaB170Homo sapiensMutation(s): 0 
Gene Names: IL23ASGRFUNQ2498/PRO5798
Find proteins for Q9NPF7 (Homo sapiens)
Explore Q9NPF7 
Go to UniProtKB:  Q9NPF7
NIH Common Fund Data Resources
PHAROS  Q9NPF7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ADNECTIND109Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
4 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.7α = 90
b = 91.7β = 90
c = 225.8γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
AMoREphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-02-28 
  • Released Date: 2012-02-01 
  • Deposition Author(s): Wei, A., Sheriff, S.

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary