5C3T Immune System date Jun 17, 2015
title Pd-1 Binding Domain From Human Pd-L1
authors K.M.Zak, G.Dubin, T.A.Holak
compound source
Molecule: Programmed Cell Death 1 Ligand 1
Chain: A
Fragment: Unp Residues 18-134
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 Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: C 2 2 21
R_factor 0.153 R_Free 0.178
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.004 54.710 84.907 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
Primary referenceStructure of the Complex of Human Programmed Death 1, PD-1, and Its Ligand PD-L1., Zak KM, Kitel R, Przetocka S, Golik P, Guzik K, Musielak B, Domling A, Dubin G, Holak TA, Structure. 2015 Oct 22. pii: S0969-2126(15)00402-5. doi:, 10.1016/j.str.2015.09.010. PMID:26602187
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (5c3t.pdb1.gz) 41 Kb
  • CSU: Contacts of Structural Units for 5C3T
  • Structure Factors (609 Kb)
  • Retrieve 5C3T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5C3T from S2C, [Save to disk]
  • Re-refined 5c3t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5C3T 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 5C3T
  • 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: [5c3t_A] [5c3t]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5C3T: [IG] [IG_like ] by SMART
    • Other resources with information on 5C3T
  • Community annotation for 5C3T at PDBWiki (http://pdbwiki.org)

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