2ADF Blood Clotting Immune System date Jul 20, 2005
title Crystal Structure And Paratope Determination Of 82d6a3, An Antithrombotic Antibody Directed Against The Von Willebrand A3-Domain
authors S.Staelens, M.A.Hadders, S.Vauterin, C.Platteau, K.Vanhoorelbeke E.G.Huizinga, H.Deckmyn
compound source
Molecule: Von Willebrand Factor
Chain: A
Fragment: A3 Domain
Synonym: Vwf
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Pet
Expression_system_plasmid: Pet15b

Molecule: 82d6a3 Igg
Chain: H
Fragment: Fab

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Secretion: Ascites

Molecule: 82d6a3 Igg
Chain: L
Fragment: Fab

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Secretion: Ascites
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.179 89.076 123.511 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ACY, GOL, SO4 enzyme
Primary referenceParatope determination of the antithrombotic antibody 82D6A3 based on the crystal structure of its complex with the von Willebrand factor A3-domain., Staelens S, Hadders MA, Vauterin S, Platteau C, De Maeyer M, Vanhoorelbeke K, Huizinga EG, Deckmyn H, J Biol Chem. 2006 Jan 27;281(4):2225-31. Epub 2005 Nov 28. PMID:16314412
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (2adf.pdb1.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 2ADF
  • CSU: Contacts of Structural Units for 2ADF
  • Likely Quarternary Molecular Structure file(s) for 2ADF
  • Structure Factors (471 Kb)
  • Retrieve 2ADF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ADF from S2C, [Save to disk]
  • Re-refined 2adf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ADF 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 2ADF
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2ADF, from MSDmotif at EBI
  • Fold representative 2adf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2adf] [2adf_H] [2adf_A] [2adf_L]
  • SWISS-PROT database: [P84751] [P01837] [P04275]
  • Domain organization of [HVM63_MOUSE] [IGKC_MOUSE] [VWF_HUMAN] by SWISSPFAM
  • Domains found in 2ADF: [IGc1] [IGv] [VWA ] by SMART
  • Other resources with information on 2ADF
  • Community annotation for 2ADF 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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