3C09 Immune System Transferase date Jan 18, 2008
title Crystal Structure The Fab Fragment Of Matuzumab (Fab72000) I With Domain III Of The Extracellular Region Of Egfr
authors K.M.Ferguson, J.Schmiedel, T.Knoechel
compound source
Molecule: Matuzumab Fab Light Chain
Chain: L, B
Engineered: Yes
Other_details: Humanmouse Chimeric Derivative Of Mouse Mon Antibody 425;
Organism_scientific: Homo Sapiens, Mus Musculus
Organism_common: Human, House Mouse
Organism_taxid: 9606,10090
Strain: ,
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090
Expression_system_cell: Mouse Myeloma Cell Line
Expression_system_vector_type: Plasmid

Molecule: Matuzumab Fab Heavy Chain
Chain: H, C
Engineered: Yes
Other_details: Humanmouse Chimeric Derivative Of Mouse Mon Antibody 425;

Organism_scientific: Homo Sapiens, Mus Musculus
Organism_common: Human, House Mouse
Organism_taxid: 9606,10090
Strain: ,
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090
Expression_system_cell: Mouse Myeloma Cell Line
Expression_system_vector_type: Plasmid

Molecule: Epidermal Growth Factor Receptor
Chain: A, D
Fragment: Segfr Domain III
Synonym: Receptor Tyrosine-Protein Kinase Erbb-1
Ec: 2.7.10.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Egfr
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pfastbac
symmetry Space Group: C 1 2 1
R_factor 0.242 R_Free 0.299
crystal
cell
length a length b length c angle alpha angle beta angle gamma
141.073 205.035 81.577 90.00 117.49 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand BMA, MAN, NAG enzyme Transferase E.C.2.7.10.1 BRENDA
Primary referenceMatuzumab binding to EGFR prevents the conformational rearrangement required for dimerization., Schmiedel J, Blaukat A, Li S, Knochel T, Ferguson KM, Cancer Cell. 2008 Apr;13(4):365-73. PMID:18394559
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (181 Kb) [Save to disk]
  • Biological Unit Coordinates (3c09.pdb1.gz) 92 Kb
  • Biological Unit Coordinates (3c09.pdb2.gz) 84 Kb
  • LPC: Ligand-Protein Contacts for 3C09
  • CSU: Contacts of Structural Units for 3C09
  • Likely Quarternary Molecular Structure file(s) for 3C09
  • Structure Factors (549 Kb)
  • Retrieve 3C09 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C09 from S2C, [Save to disk]
  • Re-refined 3c09 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3C09 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3C09
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3C09, from MSDmotif at EBI
  • Fold representative 3c09 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c09_L] [3c09_D] [3c09] [3c09_C] [3c09_B] [3c09_H] [3c09_A]
  • SWISS-PROT database: [P00533] [P01857] [P01834]
  • Domain organization of [EGFR_HUMAN] [IGHG1_HUMAN] [IGKC_HUMAN] by SWISSPFAM
  • Domains found in 3C09: [FU] [IG_like] [IGv ] by SMART
  • Other resources with information on 3C09
  • Community annotation for 3C09 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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