4YWT Membrane Protein date Mar 21, 2015
title Crystal Structure Of Full-Length Glypican-1 Core Protein Aft Controlled Crystal Dehydration To 87% Relative Humidity
authors W.Awad, K.Mani, D.T.Logan
compound source
Molecule: Glypican-1
Chain: A, B, C, D
Fragment: Unp Residues 24-527
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gpc1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
symmetry Space Group: P 1 21 1
R_factor 0.239 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.780 166.590 137.700 90.00 90.38 90.00
method X-Ray Diffractionresolution 2.38 Å
ligand CA, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural aspects of N-glycosylations and the C-terminal region in human glypican-1., Awad W, Adamczyk B, Ornros J, Karlsson NG, Mani K, Logan DT, J Biol Chem. 2015 Jul 22. pii: jbc.M115.660878. PMID:26203194
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (540 Kb) [Save to disk]
  • Biological Unit Coordinates (4ywt.pdb1.gz) 136 Kb
  • Biological Unit Coordinates (4ywt.pdb2.gz) 140 Kb
  • Biological Unit Coordinates (4ywt.pdb3.gz) 131 Kb
  • Biological Unit Coordinates (4ywt.pdb4.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 4YWT
  • CSU: Contacts of Structural Units for 4YWT
  • Structure Factors (1321 Kb)
  • Retrieve 4YWT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YWT from S2C, [Save to disk]
  • Re-refined 4ywt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YWT 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 4YWT
  • 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 4ywt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ywt_C] [4ywt] [4ywt_D] [4ywt_A] [4ywt_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4YWT
  • Community annotation for 4YWT at PDBWiki (http://pdbwiki.org)

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