5JXE Immune System date May 13, 2016
title Human Pd-1 Ectodomain Complexed With Pembrolizumab Fab
authors Z.Na, S.R.Bharath, H.Song
compound source
Molecule: Programmed Cell Death Protein 1
Chain: A, B
Fragment: Unp Residues 34-146
Synonym: Hpd-1
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdcd1, Pd1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Pembrolizumab Fab Light Chain
Chain: C, F
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Pembrolizumab Fab Heavy Chain
Chain: D, G
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
symmetry Space Group: P 65 2 2
R_factor 0.261 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.554 105.554 380.048 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.90 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for blocking PD-1-mediated immune suppression by therapeutic antibody pembrolizumab., Na Z, Yeo SP, Bharath SR, Bowler MW, Balikci E, Wang CI, Song H, Cell Res. 2017 Jan;27(1):147-150. doi: 10.1038/cr.2016.77. Epub 2016 Jun 21. PMID:27325296
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (164 Kb) [Save to disk]
  • Biological Unit Coordinates (5jxe.pdb1.gz) 83 Kb
  • Biological Unit Coordinates (5jxe.pdb2.gz) 79 Kb
  • CSU: Contacts of Structural Units for 5JXE
  • Structure Factors (1784 Kb)
  • Retrieve 5JXE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JXE from S2C, [Save to disk]
  • Re-refined 5jxe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5JXE 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 5JXE
  • 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: [5jxe_C] [5jxe_F] [5jxe_D] [5jxe_G] [5jxe] [5jxe_B] [5jxe_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JXE: [IG_like] [IGv ] by SMART
    • Other resources with information on 5JXE
  • Community annotation for 5JXE at PDBWiki (http://pdbwiki.org)

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