4AD7 Membrane Protein date Dec 22, 2011
title Crystal Structure Of Full-Length N-Glycosylated Human Glypic
authors G.Svensson, W.Awad, K.Mani, D.T.Logan
compound source
Molecule: Glypican-1
Chain: A, B, C, D
Fragment: Unp Residues 24-529
Synonym: Secreted Glypican-1
Engineered: Yes
Other_details: N-Glycosylated At Residues 79 And 116
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
Expression_system_plasmid: Pcep4
symmetry Space Group: P 1 21 1
R_factor 0.218 R_Free 0.278
length a length b length c angle alpha angle beta angle gamma
47.250 169.200 151.710 90.00 94.96 90.00
method X-Ray Diffractionresolution 2.95 Å
ligand NAG enzyme
A, D, C, B

Primary referenceCrystal Structure of N-Glycosylated Human Glypican-1 Core Protein: STRUCTURE OF TWO LOOPS EVOLUTIONARILY CONSERVED IN VERTEBRATE GLYPICAN-1., Svensson G, Awad W, Hakansson M, Mani K, Logan DT, J Biol Chem. 2012 Apr 20;287(17):14040-51. Epub 2012 Feb 20. PMID:22351761
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (535 Kb) [Save to disk]
  • Biological Unit Coordinates (4ad7.pdb1.gz) 122 Kb
  • Biological Unit Coordinates (4ad7.pdb2.gz) 143 Kb
  • Biological Unit Coordinates (4ad7.pdb3.gz) 131 Kb
  • Biological Unit Coordinates (4ad7.pdb4.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 4AD7
  • CSU: Contacts of Structural Units for 4AD7
  • Structure Factors (396 Kb)
  • Retrieve 4AD7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4AD7 from S2C, [Save to disk]
  • Re-refined 4ad7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4AD7 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 4AD7
  • 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 4AD7, from MSDmotif at EBI
  • Fold representative 4ad7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ad7_C] [4ad7_A] [4ad7] [4ad7_B] [4ad7_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4AD7
  • Community annotation for 4AD7 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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