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
  • Alignments of the sequence of 3GXE with the sequences similar proteins can be viewed for 3GXE'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 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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