5SX5

Crystal Structure of panitumumab in complex with epidermal growth factor receptor domain 3 mutant S468R.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The Panitumumab EGFR Complex Reveals a Binding Mechanism That Overcomes Cetuximab Induced Resistance.

Sickmier, E.A.Kurzeja, R.J.Michelsen, K.Vazir, M.Yang, E.Tasker, A.S.

(2016) PLoS One 11: e0163366-e0163366

  • DOI: 10.1371/journal.pone.0163366
  • Primary Citation of Related Structures:  
    5SX4, 5SX5

  • PubMed Abstract: 
  • Panitumumab and cetuximab target the epidermal growth factor receptor for the treatment of metastatic colorectal cancer. These therapies provide a significant survival benefit to patients with metastatic colorectal cancer with wild-type RAS. A single point mutation in the ectodomain of EGFR (S468R) confers acquired or secondary resistance in cetuximab treated patients, which is not observed in panitumumab-treated patients ...

    Panitumumab and cetuximab target the epidermal growth factor receptor for the treatment of metastatic colorectal cancer. These therapies provide a significant survival benefit to patients with metastatic colorectal cancer with wild-type RAS. A single point mutation in the ectodomain of EGFR (S468R) confers acquired or secondary resistance in cetuximab treated patients, which is not observed in panitumumab-treated patients. Structural and biophysical studies presented here show this mutation directly blocks cetuximab binding to EGFR domain III and describes a unique mechanism by which panitumumab uses a central cavity to accommodate this mutation.


    Organizational Affiliation

    Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, United States of America.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Panitumumab Fab Light ChainA [auth K],
C [auth L]
214Homo sapiensMutation(s): 0 
Entity Groups  
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Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Panitumumab Fab Heavy ChainD [auth H],
B [auth J]
221Homo sapiensMutation(s): 0 
Entity Groups  
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Epidermal growth factor receptorE [auth M],
F [auth N]
201Homo sapiensMutation(s): 1 
Gene Names: EGFRERBBERBB1HER1
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
M [auth J],
T [auth L],
Y [auth H]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth N],
G [auth K],
H [auth K],
I [auth K],
O [auth L],
BA [auth N],
G [auth K],
H [auth K],
I [auth K],
O [auth L],
P [auth L],
Q [auth L],
R [auth L],
S [auth L],
V [auth H],
W [auth H],
X [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth K],
K,
U [auth L],
Z [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth H],
L [auth K],
N [auth J]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.073α = 90
b = 113.106β = 90
c = 231.403γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2016-08-09 
  • Released Date: 2016-10-05 
  • Deposition Author(s): Sickmier, E.A.

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release