4DMU Structural Protein Protein Binding date Feb 08, 2012
title Crystal Structure Of The Von Willebrand Factor A3 Domain In With A Collagen III Derived Triple-Helical Peptide
authors T.H.C.Brondijk, E.G.Huizinga
compound source
Molecule: Collagen III Derived Triple-Helical Peptide
Chain: A, C, E, G, I, K
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Peptide Covers Part Of Human Colla Sequence;

Molecule: Von Willebrand Factor
Chain: B, D, F, H, J, L
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: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 6
R_factor 0.202 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
187.614 187.614 89.373 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand HYP, SO4 enzyme
Primary referenceImplications for collagen I chain registry from the structure of the collagen von Willebrand factor A3 domain complex., Brondijk TH, Bihan D, Farndale RW, Huizinga EG, Proc Natl Acad Sci U S A. 2012 Mar 21. PMID:22440751
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (513 Kb) [Save to disk]
  • Biological Unit Coordinates (4dmu.pdb1.gz) 87 Kb
  • Biological Unit Coordinates (4dmu.pdb2.gz) 87 Kb
  • Biological Unit Coordinates (4dmu.pdb3.gz) 87 Kb
  • Biological Unit Coordinates (4dmu.pdb4.gz) 87 Kb
  • Biological Unit Coordinates (4dmu.pdb5.gz) 87 Kb
  • Biological Unit Coordinates (4dmu.pdb6.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 4DMU
  • CSU: Contacts of Structural Units for 4DMU
  • Structure Factors (1549 Kb)
  • Retrieve 4DMU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DMU from S2C, [Save to disk]
  • Re-refined 4dmu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DMU 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 4DMU
  • 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 4DMU, from MSDmotif at EBI
  • Fold representative 4dmu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dmu_L] [4dmu_G] [4dmu_D] [4dmu_C] [4dmu_E] [4dmu_B] [4dmu_A] [4dmu_F] [4dmu_J] [4dmu] [4dmu_K] [4dmu_H] [4dmu_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DMU: [VWA ] by SMART
  • Alignments of the sequence of 4DMU with the sequences similar proteins can be viewed for 4DMU'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 4DMU
  • Community annotation for 4DMU at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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