4ACR Membrane Protein date Dec 17, 2011
title Crystal Structure Of N-Glycosylated, C-Terminally Truncated Glypican-1
authors G.Svensson, W.Awad, K.Mani, D.T.Logan
compound source
Molecule: Glypican-1
Chain: A, B, C, D
Fragment: Unp Residues 24-479
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 0.251 R_Free 0.292
length a length b length c angle alpha angle beta angle gamma
47.170 168.630 147.760 90.00 94.59 90.00
method X-Ray Diffractionresolution 2.55 Å
ligand NAG enzyme
note 4ACR is a representative structure
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] (531 Kb) [Save to disk]
  • Biological Unit Coordinates (4acr.pdb1.gz) 118 Kb
  • Biological Unit Coordinates (4acr.pdb2.gz) 140 Kb
  • Biological Unit Coordinates (4acr.pdb3.gz) 132 Kb
  • Biological Unit Coordinates (4acr.pdb4.gz) 143 Kb
  • LPC: Ligand-Protein Contacts for 4ACR
  • CSU: Contacts of Structural Units for 4ACR
  • Structure Factors (579 Kb)
  • Retrieve 4ACR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4ACR from S2C, [Save to disk]
  • Re-refined 4acr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ACR 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 4ACR
  • 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 4ACR, from MSDmotif at EBI
  • Fold representative 4acr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4acr_D] [4acr_A] [4acr_C] [4acr] [4acr_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4ACR
  • Community annotation for 4ACR at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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