5F2R Chaperone date Dec 02, 2015
title Crystal Structure Of Human Grp78 (70kda Heat Shock Protein 5 Atpase Domain In Complex With Amp-Pcp
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 0.199 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.958 74.549 88.414 90.00 98.15 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand ACP, MG 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] (251 Kb) [Save to disk]
  • Biological Unit Coordinates (5f2r.pdb1.gz) 124 Kb
  • Biological Unit Coordinates (5f2r.pdb2.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 5F2R
  • CSU: Contacts of Structural Units for 5F2R
  • Structure Factors (1144 Kb)
  • Retrieve 5F2R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5F2R from S2C, [Save to disk]
  • Re-refined 5f2r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5F2R 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 5F2R
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5f2r_A] [5f2r] [5f2r_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5F2R
  • Community annotation for 5F2R at PDBWiki (http://pdbwiki.org)

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