5SX5

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

PDB DOI: https://doi.org/10.2210/pdb5SX5/pdb

Classification: TRANSFERASE/IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Spodoptera frugiperda
Mutation(s): Yes

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

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 27658254 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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. 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

Depatment of Therapeutic Discovery, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, United States of America.

Macromolecule Content

Total Structure Weight: 141.23 kDa
Atom Count: 9,644
Modelled Residue Count: 1,225
Deposited Residue Count: 1,272
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Panitumumab Fab Light Chain	A [auth K], C [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Panitumumab Fab Heavy Chain	B [auth J], D [auth H]	221	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	E [auth M], F [auth N]	201	Homo sapiens	Mutation(s): 1 Gene Names: EGFR, ERBB, ERBB1, HER1 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 GTEx: ENSG00000146648
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00533
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain M [auth J] SDF format, chain T [auth L] SDF format, chain Y [auth H] MOL2 format, chain M [auth J] MOL2 format, chain T [auth L] MOL2 format, chain Y [auth H] mmCIF format, chain M [auth J] mmCIF format, chain T [auth L] mmCIF format, chain Y [auth H]	M [auth J], T [auth L], Y [auth H]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain M [auth J] Focus chain T [auth L] Focus chain Y [auth H] Interactions & Density Focus chain M [auth J] Focus chain T [auth L] Focus chain Y [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth N] SDF format, chain G [auth K] SDF format, chain H [auth K] SDF format, chain I [auth K] SDF format, chain O [auth L] SDF format, chain P [auth L] SDF format, chain Q [auth L] SDF format, chain R [auth L] SDF format, chain S [auth L] SDF format, chain V [auth H] SDF format, chain W [auth H] SDF format, chain X [auth H] MOL2 format, chain BA [auth N] MOL2 format, chain G [auth K] MOL2 format, chain H [auth K] MOL2 format, chain I [auth K] MOL2 format, chain O [auth L] MOL2 format, chain P [auth L] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth L] MOL2 format, chain S [auth L] MOL2 format, chain V [auth H] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] mmCIF format, chain BA [auth N] mmCIF format, chain G [auth K] mmCIF format, chain H [auth K] mmCIF format, chain I [auth K] mmCIF format, chain O [auth L] mmCIF format, chain P [auth L] mmCIF format, chain Q [auth L] mmCIF format, chain R [auth L] mmCIF format, chain S [auth L] mmCIF format, chain V [auth H] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H]	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		Interactions Focus chain BA [auth N] Focus chain G [auth K] Focus chain H [auth K] Focus chain I [auth K] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain BA [auth N] Focus chain G [auth K] Focus chain H [auth K] Focus chain I [auth K] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth K] SDF format, chain K SDF format, chain U [auth L] SDF format, chain Z [auth H] MOL2 format, chain J [auth K] MOL2 format, chain K MOL2 format, chain U [auth L] MOL2 format, chain Z [auth H] mmCIF format, chain J [auth K] mmCIF format, chain K mmCIF format, chain U [auth L] mmCIF format, chain Z [auth H]	J [auth K], K, U [auth L], Z [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth K] Focus chain K Focus chain U [auth L] Focus chain Z [auth H] Interactions & Density Focus chain J [auth K] Focus chain K Focus chain U [auth L] Focus chain Z [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain L [auth K] SDF format, chain N [auth J] MOL2 format, chain AA [auth H] MOL2 format, chain L [auth K] MOL2 format, chain N [auth J] mmCIF format, chain AA [auth H] mmCIF format, chain L [auth K] mmCIF format, chain N [auth J]	AA [auth H], L [auth K], N [auth J]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain L [auth K] Focus chain N [auth J] Interactions & Density Focus chain AA [auth H] Focus chain L [auth K] Focus chain N [auth J]

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 = 65.073	α = 90
b = 113.106	β = 90
c = 231.403	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

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
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary