3RNQ Immune System date Apr 22, 2011
title Crystal Structure Of The Complex Between The Extracellular D Mouse Pd-1 Mutant And Pd-L2
authors E.Lazar-Molnar, U.A.Ramagopal, S.G.Nathenson, S.C.Almo
compound source
Molecule: Programmed Cell Death 1 Ligand 2
Chain: B
Synonym: Pd-1 Ligand 2, Pd-L2, Pdcd1 Ligand 2, Programmed D Ligand 2, Butyrophilin B7-Dc, B7-Dc;
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: B7dc, Btdc, Cd273, Murine, Pdcd1lg2, Pdl2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Rosetta (De3) Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-3a

Molecule: Programmed Cell Death Protein 1
Chain: A
Synonym: Protein Pd-1, Mpd-1
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Pd1, Pdcd1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Rosetta (De3) Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-3a
symmetry Space Group: P 1 21 1
R_factor 0.183 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
36.516 79.716 51.693 90.00 105.56 90.00
method X-Ray Diffractionresolution 1.60 Å
note 3RNQ is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (3rnq.pdb1.gz) 52 Kb
  • CSU: Contacts of Structural Units for 3RNQ
  • Structure Factors (519 Kb)
  • Retrieve 3RNQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RNQ from S2C, [Save to disk]
  • Re-refined 3rnq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3RNQ 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 3RNQ
  • 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
  • 3D motif for 3RNQ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rnq_B] [3rnq_A] [3rnq]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3RNQ: [IG] [IG_like ] by SMART
    • Other resources with information on 3RNQ
  • Community annotation for 3RNQ 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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