1YY9
Structure of the extracellular domain of the epidermal growth factor receptor in complex with the Fab fragment of cetuximab/Erbitux/IMC-C225
- PDB DOI: https://doi.org/10.2210/pdb1YY9/pdb
- Classification: IMMUNE SYSTEM/Transferase
- Organism(s): Homo sapiens, Mus musculus
- Expression System: Spodoptera frugiperda, Mus musculus
- Mutation(s): No 
- Deposited: 2005-02-24 Released: 2005-04-26 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.289 
- R-Value Work: 0.239 
- R-Value Observed: 0.242 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Epidermal Growth Factor Receptor | 624 | Homo sapiens | Mutation(s): 0  Gene Names: EGFR, ERBB1 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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cetuximab Fab Light chain | B [auth C] | 213 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Cetuximab Fab Heavy chain | C [auth D] | 221 | Mus musculus, Homo sapiens This entity is chimeric | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D [auth B] | 9 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G52461YB GlyCosmos:  G52461YB GlyGen:  G52461YB |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | H [auth A], I [auth A], J [auth A], K [auth A], L [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.289 
- R-Value Work: 0.239 
- R-Value Observed: 0.242 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 77.823 | α = 90 |
b = 70.861 | β = 102.48 |
c = 147.122 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
Entry History 
Deposition Data
- Released Date: 2005-04-26  Deposition Author(s): Li, S., Schmitz, K.R., Jeffrey, P.D., Wiltzius, J.J.W., Kussie, P., Ferguson, K.M.
Revision History (Full details and data files)
- Version 1.0: 2005-04-26
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary