3BDY Hormone date Nov 15, 2007
title Dual Specific Bh1 Fab In Complex With Vegf
authors J.M.Bostrom, C.Wiesmann, B.A.Appleton
compound source
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

Molecule: Vascular Endothelial Growth Factor A
Chain: V
Fragment: Sequence Database Residues 27-135
Synonym: Vegf-A, Vascular Permeability Factor, Vpf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vegf, Vegfa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.194 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.600 197.978 77.650 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
V


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] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (3bdy.pdb1.gz) 68 Kb
  • Biological Unit Coordinates (3bdy.pdb2.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 3BDY
  • CSU: Contacts of Structural Units for 3BDY
  • Likely Quarternary Molecular Structure file(s) for 3BDY
  • Structure Factors (189 Kb)
  • Retrieve 3BDY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BDY from S2C, [Save to disk]
  • Re-refined 3bdy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BDY 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 3BDY
  • 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
  • 3D motif for 3BDY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bdy_H] [3bdy_L] [3bdy_V] [3bdy]
  • SWISS-PROT database: [P01857] [P01834] [P15692]
  • Domain organization of [IGHG1_HUMAN] [IGKC_HUMAN] [VEGFA_HUMAN] by SWISSPFAM
  • Domains found in 3BDY: [IG_like] [IGv] [PDGF ] by SMART
  • Other resources with information on 3BDY
  • Community annotation for 3BDY 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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