4AG4 Immune System Transferase date Jan 24, 2012
title Crystal Structure Of A Ddr1-Fab Complex
authors F.Carafoli, M.C.Mayer, K.Shiraishi, M.A.Pecheva, L.Y.Chan, R.Nan, B.Leitinger, E.Hohenester
compound source
Molecule: Epithelial Discoidin Domain-Containing Receptor 1
Chain: A
Fragment: Residues 29-367
Synonym: Epithelial Discoidin Domain Receptor 1, Cd167 Anti Family Member A, Cell Adhesion Kinase, Discoidin Receptor Kinase, Hgk2, Mammary Carcinoma Kinase 10, Mck-10, Protein-Tyrosine Kinase 3a, Protein-Tyrosine Kinase Rtk-6, Tyrosine Kinase Ddr, Tyrosine-Protein Kinase Cak, Cd167a;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293 C18
Expression_system_plasmid: Pcep-Pu

Molecule: Monoclonal Antibody 3e3 Heavy Chain
Chain: H
Other_details: Monoclonal Antibody Against Human Ddr1

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090

Molecule: Monoclonal Antibody 3e3 Light Chain
Chain: L
Other_details: Monoclonal Antibody Against Human Ddr1

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
symmetry Space Group: C 2 2 21
R_factor 0.2156 R_Free 0.2855
length a length b length c angle alpha angle beta angle gamma
102.510 251.480 75.370 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CA, NAG enzyme Transferase E.C. BRENDA

Primary referenceStructure of the discoidin domain receptor 1 extracellular region bound to an inhibitory fab fragment reveals features important for signaling., Carafoli F, Mayer MC, Shiraishi K, Pecheva MA, Chan LY, Nan R, Leitinger B, Hohenester E, Structure. 2012 Apr 4;20(4):688-97. Epub 2012 Apr 3. PMID:22483115
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (127 Kb) [Save to disk]
  • Biological Unit Coordinates (4ag4.pdb1.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 4AG4
  • CSU: Contacts of Structural Units for 4AG4
  • Structure Factors (181 Kb)
  • Retrieve 4AG4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4AG4 from S2C, [Save to disk]
  • Re-refined 4ag4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4AG4 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 4AG4
  • 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 4AG4, from MSDmotif at EBI
  • Fold representative 4ag4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ag4_L] [4ag4] [4ag4_A] [4ag4_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4AG4: [FA58C] [IG_like] [IGv ] by SMART
  • Other resources with information on 4AG4
  • Community annotation for 4AG4 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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