5GNI Cell Adhesion date Jul 21, 2016
title The Crystal Structure Of Pecam-1 Igl1-2 Trans-Homophilic Dim
authors M.Hu, H.Zhang, Q.Liu, Q.Hao
compound source
Molecule: Platelet Endothelial Cell Adhesion Molecule
Chain: A, B
Fragment: Unp Residues 28-232
Synonym: Pecam-1,Endocam,Gpiia',Peca1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pecam1
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
symmetry Space Group: I 2 2 2
R_factor 0.221 R_Free 0.281
length a length b length c angle alpha angle beta angle gamma
60.522 141.496 169.918 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.01 Å
Primary referenceStructural Basis for Human PECAM-1-Mediated Trans-homophilic Cell Adhesion., Hu M, Zhang H, Liu Q, Hao Q, Sci Rep. 2016 Dec 13;6:38655. doi: 10.1038/srep38655. PMID:27958302
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (5gni.pdb1.gz) 136 Kb
  • CSU: Contacts of Structural Units for 5GNI
  • Structure Factors (391 Kb)
  • Retrieve 5GNI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GNI from S2C, [Save to disk]
  • Re-refined 5gni structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5GNI 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 5GNI
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5gni from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gni] [5gni_A] [5gni_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5GNI
  • Community annotation for 5GNI at PDBWiki (http://pdbwiki.org)

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