5LGD Cell Adhesion date Jul 06, 2016
title The Cidra Domain From Mcvar1 Pfemp1 Bound To Cd36
authors F.L.Hsieh, M.K.Higgins
compound source
Molecule: Platelet Glycoprotein 4
Chain: A
Synonym: Fatty Acid Translocase,Fat,Glycoprotein Iiib,Gpiii Leukocyte Differentiation Antigen Cd36,Pas Iv,Pas-4,Platele Receptor,Platelet Glycoprotein Iv,Gpiv,Thrombospondin Recep
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd36, Gp3b, Gp4
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606

Molecule: Pfemp1 Variant 1 Of Strain Mc
Chain: B
Engineered: Yes

Organism_scientific: Plasmodium Falciparum
Organism_common: Malaria Parasite P. Falciparum
Organism_taxid: 5833
Gene: Mcvar-1 Pfemp1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.212 R_Free 0.253
length a length b length c angle alpha angle beta angle gamma
129.826 40.726 138.836 90.00 114.85 90.00
method X-Ray Diffractionresolution 2.07 Å
ligand GOL, MAN, NAG, PLM, TRS enzyme
  • cellular response to amyloid...

  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (210 Kb) [Save to disk]
  • Biological Unit Coordinates (5lgd.pdb1.gz) 203 Kb
  • LPC: Ligand-Protein Contacts for 5LGD
  • CSU: Contacts of Structural Units for 5LGD
  • Structure Factors (1113 Kb)
  • Retrieve 5LGD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LGD from S2C, [Save to disk]
  • Re-refined 5lgd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5LGD 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 5LGD
  • 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 5lgd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5lgd_A] [5lgd] [5lgd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5LGD
  • Community annotation for 5LGD at PDBWiki (http://pdbwiki.org)

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