3GXE Cell Adhesion date Apr 02, 2009
title Complex Of A Low Affinity Collagen Site With The Fibronectin Domain Pair
authors B.Sladek, I.D.Campbell, I.Vakonakis
compound source
Molecule: Fibronectin
Chain: B, A
Fragment: 8-9fni, Unp Residues 516-608
Synonym: Fn, Cold-Insoluble Globulin, Cig, Ugl-Y1, Ugl-Y2,
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fn
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_strain: X-33
Expression_system_vector_type: Genomic Integration

Molecule: Collagen Alpha-1(I) Chain
Chain: F
Fragment: Coli.260, Unp Residues 254-275
Synonym: Alpha-1 Type I Collagen
Engineered: Yes

Synthetic: Yes
Other_details: Standard Peptide Synthesis

Molecule: Collagen Alpha-1(I) Chain
Chain: E
Fragment: Coli.260, Unp Residues 254-275
Synonym: Alpha-1 Type I Collagen
Engineered: Yes

Synthetic: Yes
Other_details: Standard Peptide Synthesis
symmetry Space Group: P 31 2 1
R_factor 0.219 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.570 56.570 152.661 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand GOL, HYP, HZP, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural analysis of collagen type I interactions with human fibronectin reveals a cooperative binding mode., Erat MC, Sladek B, Campbell ID, Vakonakis I, J Biol Chem. 2013 Jun 14;288(24):17441-50. doi: 10.1074/jbc.M113.469841. Epub, 2013 May 6. PMID:23653354
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (3gxe.pdb1.gz) 37 Kb
  • Biological Unit Coordinates (3gxe.pdb2.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 3GXE
  • CSU: Contacts of Structural Units for 3GXE
  • Structure Factors (445 Kb)
  • Retrieve 3GXE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GXE from S2C, [Save to disk]
  • Re-refined 3gxe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GXE 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 3GXE
  • 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 3GXE, from MSDmotif at EBI
  • Fold representative 3gxe from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gxe_F] [3gxe_B] [3gxe] [3gxe_E] [3gxe_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3GXE: [FN1 ] by SMART
  • Other resources with information on 3GXE
  • Community annotation for 3GXE 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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