Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 87.64 kDa 
• Atom Count: 5610 
• Modelled Residue Count: 713 
• Deposited Residue Count: 762 
• Unique protein chains: 2

3QWQ

Crystal structure of the extracellular domain of the epidermal growth factor receptor in complex with an adnectin

• DOI: 10.2210/pdb3QWQ/pdb

• Classification: PROTEIN BINDING/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-28 Released: 2012-02-01 
• Deposition Author(s): Sheriff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.246 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Structures of adnectin/protein complexes reveal an expanded binding footprint.

Ramamurthy, V., Krystek, S.R., Bush, A., Wei, A., Emanuel, S.L., Das Gupta, R., Janjua, A., Cheng, L., Murdock, M., Abramczyk, B., Cohen, D., Lin, Z., Morin, P., Davis, J.H., Dabritz, M., McLaughlin, D.C., Russo, K.A., Chao, G., Wright, M.C., Jenny, V.A., Engle, L.J., Furfine, E., Sheriff, S.

(2012) Structure 20: 259-269

• PubMed: 22325775 
• DOI: 10.1016/j.str.2011.11.016
• Primary Citation of Related Structures:  
  3QWQ, 3QWR


• PubMed Abstract: 
  

Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin (¹⁰Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three ¹⁰Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the β strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these β strand interactions, indicating that these nonloop residues can expand the available binding footprint.

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Organizational Affiliation: 

Bristol-Myers Squibb Research & Development, Princeton, NJ 08543-4000, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	648	Homo sapiens	Mutation(s): 0  Gene Names: EGFR, ERBB1, ERBB, HER1 EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens) Explore P00533  Go to UniProtKB:  P00533
NIH Common Fund Data Resources
PHAROS:  P00533 GTEx:  ENSG00000146648

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADNECTIN	B	114	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, F	6		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.246 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68	α = 90
b = 72.1	β = 90
c = 262	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-28 
• Released Date: 2012-02-01 
Deposition Author(s): Sheriff, S.

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2012-02-29
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary