4R0L

Anti-canine CD28 antibody, 1C6, bound canine CD28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Anti-CD28 Antibody-Initiated Cytokine Storm in Canines.

Rosinski, S.L.Storb, R.Strong, R.K.Sale, G.E.Stone, D.M.Gewe, M.M.Friend, D.J.Abrams, V.K.Randolph-Habecker, J.Graves, S.S.

(2015) Transplant Direct 1

  • DOI: 10.1097/TXD.0000000000000516
  • Primary Citation of Related Structures:  
    4R0L

  • PubMed Abstract: 
  • CD28 signal blockade following T cell receptor activation is under intense investigation as a tolerance-inducing therapy for transplantation. Our goal is to produce a CD28-specific reagent as a therapy for the prevention of graft rejection and graft-versus-host disease in the canine model of allogeneic hematopoietic cell transplantation (HCT) ...

    CD28 signal blockade following T cell receptor activation is under intense investigation as a tolerance-inducing therapy for transplantation. Our goal is to produce a CD28-specific reagent as a therapy for the prevention of graft rejection and graft-versus-host disease in the canine model of allogeneic hematopoietic cell transplantation (HCT).


    Organizational Affiliation

    Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle Washington, 98109 ; Department of Medicine, University of Washington, Seattle, Washington, 98195.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody 1C6 Heavy chainA, D [auth H]121Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell costimulatory molecule CD28B [auth C], C [auth D]129Canis lupus familiarisMutation(s): 0 
Gene Names: CD28
Find proteins for Q9N0N8 (Canis lupus familiaris)
Explore Q9N0N8 
Go to UniProtKB:  Q9N0N8
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody 1C6 Light chainF [auth B], E [auth L]117Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth E], I [auth G]3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth F]2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth C], K [auth C], L [auth C], M [auth D], N [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.783α = 90
b = 86.783β = 90
c = 205.804γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary