3BJ5 Isomerase date Dec 03, 2007
title Alternative Conformations Of The X Region Of Human Protein D Isomerase Modulate Exposure Of The Substrate Binding B' Dom
authors L.W.Ruddock, V.D.Nguyen, R.K.Wierenga, A.M.Haapalainen
compound source
Molecule: Protein Disulfide-Isomerase
Chain: A
Fragment: B'X Domain, Unpr Residues 230-368
Synonym: Pdi, Prolyl 4-Hydroxylase Subunit Beta, Cellular T Hormone-Binding Protein, P55;
Ec: 5.3.4.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: P4hb, Erba2l, Pdi, Pdia1, Po4db
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet23a(+)
symmetry Space Group: P 31 2 1
R_factor 0.194 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.370 57.370 68.310 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand SO4 enzyme Isomerase E.C.5.3.4.1 BRENDA
note 3BJ5 is a representative structure
Primary referenceAlternative conformations of the x region of human protein disulphide-isomerase modulate exposure of the substrate binding b' domain., Nguyen VD, Wallis K, Howard MJ, Haapalainen AM, Salo KE, Saaranen MJ, Sidhu A, Wierenga RK, Freedman RB, Ruddock LW, Williamson RA, J Mol Biol. 2008 Nov 28;383(5):1144-55. Epub 2008 Sep 9. PMID:18801374
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (3bj5.pdb1.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 3BJ5
  • CSU: Contacts of Structural Units for 3BJ5
  • Likely Quarternary Molecular Structure file(s) for 3BJ5
  • Structure Factors (99 Kb)
  • Retrieve 3BJ5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BJ5 from S2C, [Save to disk]
  • Re-refined 3bj5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BJ5 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 3BJ5
  • 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
  • 3D motif for 3BJ5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bj5] [3bj5_A]
  • SWISS-PROT database: [P07237]
  • Domain organization of [PDIA1_HUMAN] by SWISSPFAM
  • Other resources with information on 3BJ5
  • Community annotation for 3BJ5 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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