5SX4 | pdb_00005sx4

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

PDB DOI: https://doi.org/10.2210/pdb5SX4/pdb

Classification: TRANSFERASE/IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Spodoptera frugiperda
Mutation(s): No

Deposited: 2016-08-09 Released: 2016-10-05
Deposition Author(s): Sickmier, E.A., Kurzeja, R.J.M., Michelsen, K., Mukta, V., Yang, E., Tasker, A.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.266 (Depositor), 0.267 (DCC)
R-Value Work:
0.223 (Depositor), 0.223 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0163366
Primary Citation 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: 140.07 kDa
Atom Count: 9,504
Modeled Residue Count: 1,218
Deposited Residue Count: 1,272
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Panitumumab Fab Light Chain	A [auth I], C [auth L]	214	Homo sapiens	Mutation(s): 0

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| 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

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| 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): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 P [auth H] SDF format, chain K [auth J] MOL2 format, chain P [auth H] MOL2 format, chain K [auth J] mmCIF format, chain P [auth H] mmCIF format, chain K [auth J]	K [auth J], P [auth H]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain K [auth J] Focus chain P [auth H] Interactions & Density Focus chain K [auth J] Focus chain P [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth N] SDF format, chain O [auth L] SDF format, chain N [auth L] SDF format, chain M [auth L] SDF format, chain L SDF format, chain I SDF format, chain H [auth I] SDF format, chain G [auth I] MOL2 format, chain R [auth N] MOL2 format, chain O [auth L] MOL2 format, chain N [auth L] MOL2 format, chain M [auth L] MOL2 format, chain L MOL2 format, chain I MOL2 format, chain H [auth I] MOL2 format, chain G [auth I] mmCIF format, chain R [auth N] mmCIF format, chain O [auth L] mmCIF format, chain N [auth L] mmCIF format, chain M [auth L] mmCIF format, chain L mmCIF format, chain I mmCIF format, chain H [auth I] mmCIF format, chain G [auth I]	G [auth I] H [auth I] I L M [auth L] G [auth I], H [auth I], I, L, M [auth L], N [auth L], O [auth L], R [auth N]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth I] Focus chain H [auth I] Focus chain I Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain R [auth N] Interactions & Density Focus chain G [auth I] Focus chain H [auth I] Focus chain I Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain R [auth N]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth I] MOL2 format, chain J [auth I] mmCIF format, chain J [auth I]	J [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth I] Interactions & Density Focus chain J [auth I]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth H] MOL2 format, chain Q [auth H] mmCIF format, chain Q [auth H]	Q [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth H] Interactions & Density Focus chain Q [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.266 (Depositor), 0.267 (DCC)
R-Value Work: 0.223 (Depositor), 0.223 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.273	α = 90
b = 113.184	β = 90
c = 232.443	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

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: 2024-10-16
Changes: Structure summary