3HXO Blood Clotting Blood Clotting Regulator date Jun 21, 2009
title Crystal Structure Of Von Willebrand Factor (Vwf) A1 Domain I With Dna Aptamer Arc1172, An Inhibitor Of Vwf-Platelet Bind
authors R.H.Huang, J.E.Sadler, D.H.Fremont, J.L.Diener, R.G.Schaub
compound source
Molecule: Von Willebrand Factor
Chain: A
Fragment: Von Willebrand Factor (Vwf) A1 Domain (Residues 1
Synonym: Vwf, Von Willebrand Antigen 2, Von Willebrand Anti
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vwf, F8vwf
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Aptamer Arc1172
Chain: B
Fragment: Aptamer Arc1172
Engineered: Yes

Synthetic: Yes
Other_details: Arc1172 Is A Dna Oligonucleotides That Bind Target Molecules, Identified By Selection In Vitro From Lar
Sequence Libraries (Termed Selex: Systematic Evolution Of L Exponential Enrichment)
symmetry Space Group: P 21 21 21
R_factor 0.228 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.093 66.354 108.749 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
Primary referenceA structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1., Huang RH, Fremont DH, Diener JL, Schaub RG, Sadler JE, Structure. 2009 Nov 11;17(11):1476-84. PMID:19913482
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (3hxo.pdb1.gz) 114 Kb
  • CSU: Contacts of Structural Units for 3HXO
  • Structure Factors (182 Kb)
  • Retrieve 3HXO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HXO from S2C, [Save to disk]
  • Re-refined 3hxo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HXO 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 3HXO
  • 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 3HXO, from MSDmotif at EBI
  • Fold representative 3hxo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hxo_B] [3hxo_A] [3hxo]
  • SWISS-PROT database: [P04275]
  • Domain organization of [VWF_HUMAN] by SWISSPFAM
  • Domain found in 3HXO: [VWA ] by SMART
  • Alignments of the sequence of 3HXO with the sequences similar proteins can be viewed for 3HXO's classification [VWF_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 [VWF_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3HXO
  • Community annotation for 3HXO 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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