5B8C Immune System date Jun 14, 2016
title High Resolution Structure Of The Human Pd-1 In Complex With Pembrolizumab Fv
authors S.Horita, T.Shimamura, S.Iwata, N.Nomura
compound source
Molecule: Pembrolizumab Light Chain Variable Region (Pemvl)
Chain: A, D, G, J
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Brevibacillus Choshinensis
Expression_system_taxid: 54911

Molecule: Pembrolizumab Heavy Chain Variable Region (Pemvh)
Chain: B, E, H, K
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Brevibacillus Choshinensis
Expression_system_taxid: 54911

Molecule: Programmed Cell Death Protein 1
Chain: C, F, I, L
Synonym: Hpd-1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdcd1, Pd1
Expression_system: Brevibacillus Choshinensis
Expression_system_taxid: 54911
symmetry Space Group: P 21 21 21
R_factor 0.184 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
143.680 143.130 76.550 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
Gene
Ontology
ChainFunctionProcessComponent
F, C, I, L


Primary referenceHigh-resolution crystal structure of the therapeutic antibody pembrolizumab bound to the human PD-1., Horita S, Nomura Y, Sato Y, Shimamura T, Iwata S, Nomura N, Sci Rep. 2016 Oct 13;6:35297. doi: 10.1038/srep35297. PMID:27734966
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (466 Kb) [Save to disk]
  • Biological Unit Coordinates (5b8c.pdb1.gz) 117 Kb
  • Biological Unit Coordinates (5b8c.pdb2.gz) 115 Kb
  • Biological Unit Coordinates (5b8c.pdb3.gz) 115 Kb
  • Biological Unit Coordinates (5b8c.pdb4.gz) 116 Kb
  • CSU: Contacts of Structural Units for 5B8C
  • Structure Factors (1452 Kb)
  • Retrieve 5B8C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5B8C from S2C, [Save to disk]
  • Re-refined 5b8c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5B8C 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 5B8C
  • 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 5b8c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5b8c_K] [5b8c_B] [5b8c_A] [5b8c_G] [5b8c_F] [5b8c_L] [5b8c_I] [5b8c_J] [5b8c_C] [5b8c_E] [5b8c_H] [5b8c_D] [5b8c]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5B8C: [IGv ] by SMART
  • Other resources with information on 5B8C
  • Community annotation for 5B8C at PDBWiki (http://pdbwiki.org)

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