5C14 Cell Adhesion date Jun 12, 2015
title Crystal Structure Of Pecam-1 D1d2 Domain
authors D.Zhou, C.Paddock, P.Newman, J.Zhu
compound source
Molecule: Platelet Endothelial Cell Adhesion Molecule
Chain: A
Fragment: D1d2 Domain (Unp Residues 28-229)
Synonym: Pecam-1,Endocam,Gpiia',Peca1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pecam1
Expression_system: Drosophila
Expression_system_taxid: 7215

Molecule: Platelet Endothelial Cell Adhesion Molecule
Chain: B
Fragment: D1d2 Domain (Unp Residues 28-229)
Synonym: Pecam-1,Endocam,Gpiia',Peca1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pecam1
Expression_system: Drosophila
Expression_system_taxid: 7215
symmetry Space Group: I 41 2 2
R_factor 0.238 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.010 104.010 281.834 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CU, GOL, MSE, NAG, TRS enzyme
Primary referenceStructural basis for PECAM-1 homophilic binding., Paddock C, Zhou D, Lertkiatmongkol P, Newman PJ, Zhu J, Blood. 2015 Dec 23. pii: blood-2015-07-660092. PMID:26702061
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (5c14.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (5c14.pdb2.gz) 73 Kb
  • Biological Unit Coordinates (5c14.pdb3.gz) 287 Kb
  • LPC: Ligand-Protein Contacts for 5C14
  • CSU: Contacts of Structural Units for 5C14
  • Structure Factors (291 Kb)
  • Retrieve 5C14 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5C14 from S2C, [Save to disk]
  • Re-refined 5c14 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5C14 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 5C14
  • 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
  • Fold representative 5c14 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5c14_A] [5c14] [5c14_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5C14: [IG ] by SMART
  • Other resources with information on 5C14
  • Community annotation for 5C14 at PDBWiki (http://pdbwiki.org)

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