3ZQK Blood Clotting date Jun 09, 2011
title Von Willebrand Factor A2 Domain With Calcium
authors A.J.Jakobi, E.G.Huizinga
compound source
Molecule: Von Willebrand Factor
Chain: A, B, C
Fragment: A2 Domain, Residues 1478-1674
Synonym: Vwf, Von Willebrand Antigen 2, Von Willebrand Anti
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293-Ebna1-S
symmetry Space Group: C 1 2 1
R_factor 0.1549 R_Free 0.1996
length a length b length c angle alpha angle beta angle gamma
156.020 35.540 88.460 90.00 96.34 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand CA, GOL, NAG enzyme
Primary referenceCalcium modulates force sensing by the von Willebrand factor A2 domain., Jakobi AJ, Mashaghi A, Tans SJ, Huizinga EG, Nat Commun. 2011 Jul 12;2:385. doi: 10.1038/ncomms1385. PMID:21750539
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (202 Kb) [Save to disk]
  • Biological Unit Coordinates (3zqk.pdb1.gz) 68 Kb
  • Biological Unit Coordinates (3zqk.pdb2.gz) 65 Kb
  • Biological Unit Coordinates (3zqk.pdb3.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 3ZQK
  • CSU: Contacts of Structural Units for 3ZQK
  • Structure Factors (396 Kb)
  • Retrieve 3ZQK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZQK from S2C, [Save to disk]
  • Re-refined 3zqk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZQK 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 3ZQK
  • 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 3ZQK, from MSDmotif at EBI
  • Fold representative 3zqk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zqk_C] [3zqk_A] [3zqk_B] [3zqk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3ZQK: [VWA ] by SMART
  • Alignments of the sequence of 3ZQK with the sequences similar proteins can be viewed for 3ZQK'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 3ZQK
  • Community annotation for 3ZQK at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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