4ZQK Immune System date May 10, 2015
title Structure Of The Complex Of Human Programmed Death-1 (Pd-1) Ligand Pd-L1.
authors K.M.Zak, G.Dubin, T.A.Holak
compound source
Molecule: Programmed Cell Death 1 Ligand 1
Chain: A
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

Molecule: Programmed Cell Death Protein 1
Chain: B
Fragment: Unp Residues 33-150
Synonym: Hpd-1
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdcd1, Pd1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: P 31 2 1
R_factor 0.207 R_Free 0.253
length a length b length c angle alpha angle beta angle gamma
70.862 70.862 114.367 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.45 Å
ligand NA enzyme

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] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (4zqk.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 4ZQK
  • CSU: Contacts of Structural Units for 4ZQK
  • Structure Factors (824 Kb)
  • Retrieve 4ZQK in mmCIF format [Save to disk]
  • Re-refined 4zqk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ZQK 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 4ZQK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 4zqk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4zqk_B] [4zqk_A] [4zqk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4ZQK: [IG] [IG_like] [IGv ] by SMART
  • Other resources with information on 4ZQK
  • Community annotation for 4ZQK at PDBWiki (http://pdbwiki.org)

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