5F0X Chaperone date Nov 28, 2015
title Crystal Structure Of Human Grp78 (70kda Heat Shock Protein 5 Atpase Domain In Complex With 2'-Deoxy-Adp And Inorganic Ph
authors S.J.Hughes, T.Antoshchenko, J.H.Song, J.Pizarro, H.W.Park
compound source
Molecule: 78 Kda Glucose-Regulated Protein
Chain: A, B
Fragment: Atpase Domain (Unp Residues 26-407)
Synonym: Grp-78, Endoplasmic Reticulum Lumenal Ca(2+)-Bindi Grp78, Heat Shock 70 Kda Protein 5, Immunoglobulin Heavy Ch Binding Protein, Bip;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hspa5, Grp78
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1 21 1
R_factor 0.174 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.347 74.448 85.882 90.00 97.67 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand DAT, DTP, MG, PO4 enzyme
Primary referenceProbing the ATP Site of GRP78 with Nucleotide Triphosphate Analogs., Hughes SJ, Antoshchenko T, Chen Y, Lu H, Pizarro JC, Park HW, PLoS One. 2016 May 4;11(5):e0154862. doi: 10.1371/journal.pone.0154862., eCollection 2016. PMID:27144892
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (261 Kb) [Save to disk]
  • Biological Unit Coordinates (5f0x.pdb1.gz) 129 Kb
  • Biological Unit Coordinates (5f0x.pdb2.gz) 129 Kb
  • LPC: Ligand-Protein Contacts for 5F0X
  • CSU: Contacts of Structural Units for 5F0X
  • Structure Factors (2503 Kb)
  • Retrieve 5F0X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5F0X from S2C, [Save to disk]
  • Re-refined 5f0x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5F0X 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 5F0X
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5f0x] [5f0x_B] [5f0x_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5F0X
  • Community annotation for 5F0X at PDBWiki (http://pdbwiki.org)

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