1YY9

Structure of the extracellular domain of the epidermal growth factor receptor in complex with the Fab fragment of cetuximab/Erbitux/IMC-C225

Structural Biology Knowledgebase: 1YY9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.239

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YY9

Classification: IMMUNE SYSTEM / Transferase

Total Structure Weight: 120236.70

Macromolecule Entities
Molecule Chains Length Organism Details
Epidermal Growth Factor Receptor A 624 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: UNP residues 25-642
Mutation: S474K, E610R
Gene Name(s): EGFR Gene View ERBB ERBB1 HER1
Cetuximab Fab Light chain C 213 Homo sapiens Mus musculus
Cetuximab Fab Heavy chain D 221 Homo sapiens Mus musculus

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDG
Query on NDG

A, D 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.239
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 77.82 α = 90.00
b = 70.86 β = 102.48
c = 147.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-24
  • 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

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4