5J8O Immune System date Apr 08, 2016
title Structure Of Human Programmed Cell Death 1 Ligand 1 (Pd-L1) Molecular Mass Inhibitor
authors K.M.Zak, P.Grudnik, K.Guzik, B.J.Zieba, B.Musielak, P.Doemling, G. T.A.Holak
compound source
Molecule: Programmed Cell Death 1 Ligand 1
Chain: A, B
Synonym: Programmed Death Ligand 1,B7 Homolog 1,B7-H1
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd274, B7h1, Pdcd1l1, Pdcd1lg1, Pdl1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 2 21 21
R_factor 0.241 R_Free 0.305
crystal
cell
length a length b length c angle alpha angle beta angle gamma
34.313 55.182 141.773 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 6GZ enzyme
Primary referenceStructural basis for small molecule targeting of the programmed death ligand 1 (PD-L1)., Zak KM, Grudnik P, Guzik K, Zieba BJ, Musielak B, Domling A, Dubin G, Holak TA, Oncotarget. 2016 Apr 13. doi: 10.18632/oncotarget.8730. PMID:27083005
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (5j8o.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 5J8O
  • CSU: Contacts of Structural Units for 5J8O
  • Structure Factors (798 Kb)
  • Retrieve 5J8O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5J8O from S2C, [Save to disk]
  • Re-refined 5j8o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5J8O 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 5J8O
  • 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: [5j8o_A] [5j8o_B] [5j8o]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5J8O: [IG] [IG_like ] by SMART
    • Other resources with information on 5J8O
  • Community annotation for 5J8O at PDBWiki (http://pdbwiki.org)

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