3Q13 Cell Adhesion date Dec 16, 2010
title The Structure Of The Ca2+-Binding, Glycosylated F-Spondin Do Spondin, A C2-Domain Variant From Extracellular Matrix
authors K.Tan, J.Lawler
compound source
Molecule: Spondin-1
Chain: A
Fragment: Unp Residues 191-434
Synonym: F-Spondin, Vascular Smooth Muscle Cell Growth-Prom Factor;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Homo Sapiens, Kiaa0762, Spon1, Vsgp
Expression_system: Drosophila
Expression_system_taxid: 32281
Expression_system_strain: Drosophila Schneider 2 Cell
Expression_system_cell: Schneider 2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmtbip V5-Hisa
symmetry Space Group: P 6 2 2
R_factor 0.167 R_Free 0.210
length a length b length c angle alpha angle beta angle gamma
120.244 120.244 86.362 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.95 Å
ligand ACT, BMA, CA, NAG, SO4 enzyme
Primary referenceThe structure of the Ca2+-binding, glycosylated F-spondin domain of F-spondin - A C2-domain variant in an extracellular matrix protein., Tan K, Lawler J, BMC Struct Biol. 2011 May 10;11:22. PMID:21569239
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (3q13.pdb1.gz) 91 Kb
  • Biological Unit Coordinates (3q13.pdb2.gz) 180 Kb
  • LPC: Ligand-Protein Contacts for 3Q13
  • CSU: Contacts of Structural Units for 3Q13
  • Structure Factors (405 Kb)
  • Retrieve 3Q13 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3Q13 from S2C, [Save to disk]
  • Re-refined 3q13 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3Q13 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 3Q13
  • 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 3Q13, from MSDmotif at EBI
  • Fold representative 3q13 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3q13] [3q13_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3Q13
  • Community annotation for 3Q13 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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