3PPY Cell Adhesion date Nov 25, 2010
title Crystal Structure Of The D1596an1602a Double Mutant Of An E Vwf A2 Domain (N1493c And C1670s)
authors M.Zhou, X.Dong, C.Zhong, J.Ding
compound source
Molecule: Von Willebrand Factor
Chain: A
Fragment: Vwf A2 Domain, Unp Residues 1488-1674
Synonym: Vwf, Von Willebrand Antigen 2, Von Willebrand Anti
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: F8vwf, Vwf
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 65
R_factor 0.201 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.516 72.516 76.140 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand NA enzyme
Primary referenceA novel calcium-binding site of von Willebrand factor A2 domain regulates its cleavage by ADAMTS13., Zhou M, Dong X, Baldauf C, Chen H, Zhou Y, Springer TA, Luo X, Zhong C, Grater F, Ding J, Blood. 2011 Apr 28;117(17):4623-31. Epub 2011 Mar 8. PMID:21385852
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (3ppy.pdb1.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 3PPY
  • CSU: Contacts of Structural Units for 3PPY
  • Structure Factors (115 Kb)
  • Retrieve 3PPY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PPY from S2C, [Save to disk]
  • Re-refined 3ppy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PPY 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 3PPY
  • 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 3PPY, from MSDmotif at EBI
  • Fold representative 3ppy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ppy_A] [3ppy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PPY: [VWA ] by SMART
  • Alignments of the sequence of 3PPY with the sequences similar proteins can be viewed for 3PPY'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 3PPY
  • Community annotation for 3PPY 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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