6ARU

Structure of Cetuximab Fab mutant in complex with EGFR extracellular domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report



Literature

Structure of Cetuximab Fab mutant in complex with EGFR extracellular domain

Christie, M.Christ, D.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epidermal growth factor receptorA622Homo sapiensMutation(s): 0 
Gene Names: EGFRERBBERBB1HER1
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
NIH Common Fund Data Resources
PHAROS  P00533
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cetuximab mutant light chain,Uncharacterized proteinB214Homo sapiensMutation(s): 0 
Find proteins for Q8TCD0 (Homo sapiens)
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Go to UniProtKB:  Q8TCD0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cetuximab mutant heavy chain Fab fragment,Immunoglobulin gamma-1 heavy chainC222Homo sapiensMutation(s): 0 
Find proteins for P0DOX5 (Homo sapiens)
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Go to UniProtKB:  P0DOX5
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)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
8 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-glucopyranose
E
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 
A, C
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: 3.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.495α = 90
b = 70.444β = 100.95
c = 149.079γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDE160100608
Australian Research Council (ARC)AustraliaDP160104915

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary