3FN3 Immune System date Dec 23, 2008
title Dimeric Structure Of Pd-L1
authors Y.Chen, F.Gao, P.Liu, F.Chu, J.Qi, G.F.Gao
compound source
Molecule: Programmed Cell Death 1 Ligand 1
Chain: A, B
Fragment: Extracellular Domain
Synonym: B7-H1, Pd-L1, Programmed Death Ligand 1, Pdcd1 Lig Homolog 1;
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_vector_type: Plasmid
Expression_system_plasmid: Pet21a
symmetry Space Group: C 2 2 21
R_factor 0.226 R_Free 0.296
length a length b length c angle alpha angle beta angle gamma
71.865 91.373 140.316 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
Primary referenceA dimeric structure of PD-L1: functional units or evolutionary relics?, Chen Y, Liu P, Gao F, Cheng H, Qi J, Gao GF, Protein Cell. 2010 Feb;1(2):153-60. Epub 2010 Feb 6. PMID:21203985
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (3fn3.pdb1.gz) 70 Kb
  • CSU: Contacts of Structural Units for 3FN3
  • Structure Factors (198 Kb)
  • Retrieve 3FN3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FN3 from S2C, [Save to disk]
  • Re-refined 3fn3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FN3 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 3FN3
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3FN3, from MSDmotif at EBI
  • Fold representative 3fn3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fn3] [3fn3_A] [3fn3_B]
  • SWISS-PROT database: [Q9NZQ7]
  • Domain organization of [PD1L1_HUMAN] by SWISSPFAM
  • Domains found in 3FN3: [IG] [IG_like ] by SMART
  • Other resources with information on 3FN3
  • Community annotation for 3FN3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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