4GYX Structural Protein, Blood Clotting date Sep 05, 2012
title The Von Willebrand Factor A3 Domain Binding Region Of Type I Collagen Stabilized By The Cysteine Knot
authors S.P.Boudko, H.P.Bachinger
compound source
Molecule: Type III Collagen Fragment In A Host Peptide Stab The Cysteine Knot;
Chain: A, B, C
Fragment: Von Willebrand Factor Binding Fragment
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: This Sequence Contains Two Fragments Of Huma
III Collagen: The Von Willebrand Factor A3 Domain Binding R The Cysteine Knot
symmetry Space Group: P 1 21 1
R_factor 0.176 R_Free 0.222
length a length b length c angle alpha angle beta angle gamma
19.070 26.990 64.120 90.00 92.48 90.00
method X-Ray Diffractionresolution 1.49 Å
ligand HYP enzyme
Primary referenceThe NC2 domain of type IX collagen determines the chain register of the triple helix., Boudko SP, Bachinger HP, J Biol Chem. 2012 Nov 6. PMID:23132862
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (31 Kb) [Save to disk]
  • Biological Unit Coordinates (4gyx.pdb1.gz) 25 Kb
  • LPC: Ligand-Protein Contacts for 4GYX
  • CSU: Contacts of Structural Units for 4GYX
  • Structure Factors (134 Kb)
  • Retrieve 4GYX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GYX from S2C, [Save to disk]
  • Re-refined 4gyx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GYX 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 4GYX
  • 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 4GYX, from MSDmotif at EBI
  • Fold representative 4gyx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gyx_A] [4gyx_B] [4gyx] [4gyx_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4GYX
  • Community annotation for 4GYX at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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