4D90 Cell Adhesion date Jan 11, 2012
title Crystal Structure Of Del-1 Egf Domains
authors Q.Chen, T.Schurpf, T.Springer, J.Wang
compound source
Molecule: Egf-Like Repeat And Discoidin I-Like Domain-Conta Protein 3;
Chain: A, B
Fragment: Egf Domains
Synonym: Developmentally-Regulated Endothelial Cell Locus 1 Integrin-Binding Protein Del1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Del-1, Del1, Edil3
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: 293 Gnti(-)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plexm
symmetry Space Group: P 32
R_factor 0.204 R_Free 0.259
length a length b length c angle alpha angle beta angle gamma
82.680 82.680 56.422 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand CA, FUC, NAG, NGA enzyme
A, B

Primary referenceThe RGD finger of Del-1 is a unique structural feature critical for integrin binding., Schurpf T, Chen Q, Liu JH, Wang R, Springer TA, Wang JH, FASEB J. 2012 May 17. PMID:22601780
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (4d90.pdb1.gz) 22 Kb
  • Biological Unit Coordinates (4d90.pdb2.gz) 22 Kb
  • Biological Unit Coordinates (4d90.pdb3.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 4D90
  • CSU: Contacts of Structural Units for 4D90
  • Structure Factors (211 Kb)
  • Retrieve 4D90 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D90 from S2C, [Save to disk]
  • Re-refined 4d90 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4D90 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 4D90
  • 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 4D90, from MSDmotif at EBI
  • Fold representative 4d90 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d90_B] [4d90] [4d90_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4D90: [EGF_CA] [EGF_like ] by SMART
  • Other resources with information on 4D90
  • Community annotation for 4D90 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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