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
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] [EGF_CA ] by SMART
  • Alignments of the sequence of 4D90 with the sequences similar proteins can be viewed for 4D90'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 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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