3N85 Transferase Immune System date May 27, 2010
title Crystallographic Trimer Of Her2 Extracellular Regions In Com Tryptophan-Rich Antibody Fragment
authors C.Eigenbrot
compound source
Molecule: Receptor Tyrosine-Protein Kinase Erbb-2
Chain: A
Fragment: Unp Residues 23-646
Synonym: P185erbb2, Proto-Oncogene C-Erbb-2, Proto-Oncogene Tyrosine Kinase-Type Cell Surface Receptor Her2, Metastatic Node Gene 19 Protein, Mln 19;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Erbb2, Her2, Mln19, Neu, Ngl
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029

Molecule: Fab37 Light Chain
Chain: L
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Light Chain (Chain Id L) Was Selected From A Library Based On A Human Kappa Light Chain Displayed On Pha

Molecule: Fab37 Heavy Chain
Chain: H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Heavy Chain (Chain Id H) Was Selected From A Library Based On A Human Heavy Chain Displayed On Phage
symmetry Space Group: P 63 2 2
R_factor 0.206 R_Free 0.230
length a length b length c angle alpha angle beta angle gamma
182.220 182.220 330.851 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.20 Å
ligand BMA, CL, FUC, NAG, SO4 enzyme Transferase E.C. BRENDA
Primary referenceStructure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine., Fisher RD, Ultsch M, Lingel A, Schaefer G, Shao L, Birtalan S, Sidhu SS, Eigenbrot C, J Mol Biol. 2010 Sep 10;402(1):217-29. Epub 2010 Jul 21. PMID:20654626
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (358 Kb) [Save to disk]
  • Biological Unit Coordinates (3n85.pdb1.gz) 1038 Kb
  • LPC: Ligand-Protein Contacts for 3N85
  • CSU: Contacts of Structural Units for 3N85
  • Structure Factors (710 Kb)
  • Retrieve 3N85 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3N85 from S2C, [Save to disk]
  • Re-refined 3n85 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3N85 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 3N85
  • 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 3N85, from MSDmotif at EBI
  • Fold representative 3n85 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3n85_H] [3n85] [3n85_A] [3n85_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3N85: [FU] [IGc1] [IGv ] by SMART
  • Alignments of the sequence of 3N85 with the sequences similar proteins can be viewed for 3N85's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3N85
  • Community annotation for 3N85 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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