3BE1 Transferase date Nov 15, 2007
title Dual Specific Bh1 Fab In Complex With The Extracellular Doma Her2erbb-2
authors J.M.Bostrom, C.Wiesmann, B.A.Appleton
compound source
Molecule: Receptor Tyrosine-Protein Kinase Erbb-2
Chain: A
Fragment: Sequence Database Residues 23-646
Synonym: P185erbb2, C-Erbb-2, Neu Proto-Oncogene, Tyrosine Type Cell Surface Receptor Her2, Mln 19, Cd340 Antigen;
Ec: 2.7.10.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Erbb2, Her2, Neu, Ngl
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Chinese Hamster Ovary

Molecule: Fab Fragment-Heavy Chain
Chain: H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Fab Fragment-Light Chain
Chain: L
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.236 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.324 115.056 208.171 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand MES, NAG enzyme Transferase E.C.2.7.10.1 BRENDA
Primary referenceVariants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site., Bostrom J, Yu SF, Kan D, Appleton BA, Lee CV, Billeci K, Man W, Peale F, Ross S, Wiesmann C, Fuh G, Science. 2009 Mar 20;323(5921):1610-4. PMID:19299620
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (168 Kb) [Save to disk]
  • Biological Unit Coordinates (3be1.pdb1.gz) 160 Kb
  • LPC: Ligand-Protein Contacts for 3BE1
  • CSU: Contacts of Structural Units for 3BE1
  • Likely Quarternary Molecular Structure file(s) for 3BE1
  • Structure Factors (263 Kb)
  • Retrieve 3BE1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BE1 from S2C, [Save to disk]
  • Re-refined 3be1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BE1 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 3BE1
  • 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 3BE1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1b3be1, region E:179-412 [Jmol] [rasmolscript] [script source]
  • Fold representative 3be1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3be1] [3be1_H] [3be1_L] [3be1_A]
  • SWISS-PROT database: [P04626] [P01857] [P01834]
  • Domain organization of [ERBB2_HUMAN] [IGHG1_HUMAN] [IGKC_HUMAN] by SWISSPFAM
  • Domains found in 3BE1: [FU] [IGc1] [IGv ] by SMART
  • Alignments of the sequence of 3BE1 with the sequences similar proteins can be viewed for 3BE1's classification [ERBB2_HUMAN] [IGHG1_HUMAN] [IGKC_HUMAN] 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 [ERBB2_HUMAN] [IGHG1_HUMAN] [IGKC_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3BE1
  • Community annotation for 3BE1 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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