5NIR Structural Protein date Mar 27, 2017
title Crystal Structure Of Collagen 2a Vwc Domain
authors G.Fischer, E.Blythe, M.Hyvonen
compound source
Molecule: Collagen Alpha-1(II) Chain
Chain: A, B
Synonym: Alpha-1 Type II Collagen
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Col2a1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_plasmid: Phat3
symmetry Space Group: P 21 21 21
R_factor 0.209 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
31.930 60.160 86.420 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.74 Å
ligand EDO, P33, PEG, PG4 enzyme
Primary referenceStructural analyses of von Willebrand factor C domains of collagen 2A and CCN3 reveal an alternative mode of binding to bone morphogenetic protein-2., Xu ER, Blythe EE, Fischer G, Hyvonen M, J Biol Chem. 2017 Jul 28;292(30):12516-12527. doi: 10.1074/jbc.M117.788992. Epub , 2017 Jun 5. PMID:28584056
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (32 Kb) [Save to disk]
  • Biological Unit Coordinates (5nir.pdb1.gz) 14 Kb
  • Biological Unit Coordinates (5nir.pdb2.gz) 14 Kb
  • LPC: Ligand-Protein Contacts for 5NIR
  • CSU: Contacts of Structural Units for 5NIR
  • Structure Factors (567 Kb)
  • Retrieve 5NIR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NIR from S2C, [Save to disk]
  • Re-refined 5nir structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5NIR 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 5NIR
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5nir_A] [5nir_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5NIR
  • Community annotation for 5NIR at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science