3BIK Immune System date Nov 30, 2007
title Crystal Structure Of The Pd-1pd-L1 Complex
authors D.Y.Lin, Y.Tanaka, M.Iwasaki, A.G.Gittis, H.P.Su, B.Mikami, T.Okaz T.Honjo, N.Minato, D.N.Garboczi
compound source
Molecule: Programmed Cell Death 1 Ligand 1
Chain: A
Fragment: Extracellular Region
Synonym: Programmed Death Ligand 1, Pd-L1, Pdcd1 Ligand 1, 1, B7-H1, Cd274 Antigen;
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
Expression_system_strain: Rosetta 2 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1

Molecule: Programmed Cell Death Protein 1
Chain: B, C
Fragment: Extracellular Domain
Synonym: Protein Pd-1, Mpd-1, Cd279 Antigen
Engineered: Yes
Mutation: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Pdcd1, Pd1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1
symmetry Space Group: P 21 21 21
R_factor 0.211 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.460 63.940 159.920 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
C, B


Primary referenceThe PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors., Lin DY, Tanaka Y, Iwasaki M, Gittis AG, Su HP, Mikami B, Okazaki T, Honjo T, Minato N, Garboczi DN, Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):3011-6. Epub 2008 Feb 14. PMID:18287011
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk]
  • Biological Unit Coordinates (3bik.pdb1.gz) 115 Kb
  • Biological Unit Coordinates (3bik.pdb2.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 3BIK
  • CSU: Contacts of Structural Units for 3BIK
  • Likely Quarternary Molecular Structure file(s) for 3BIK
  • Structure Factors (141 Kb)
  • Retrieve 3BIK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BIK from S2C, [Save to disk]
  • Re-refined 3bik structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BIK 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 3BIK
  • 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
  • 3D motif for 3BIK, from MSDmotif at EBI
  • Fold representative 3bik from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bik_A] [3bik_B] [3bik] [3bik_C]
  • SWISS-PROT database: [Q9NZQ7] [Q02242]
  • Domain organization of [PD1L1_HUMAN] [PDCD1_MOUSE] by SWISSPFAM
  • Domains found in 3BIK: [IG] [IG_like ] by SMART
  • Other resources with information on 3BIK
  • Community annotation for 3BIK at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science