3SBW Immune System date Jun 06, 2011
title Crystal Structure Of The Complex Between The Extracellular D Mouse Pd-1 Mutant And Human Pd-L1
authors E.Lazar-Molnar, U.A.Ramagopal, E.Cao, S.G.Nathenson, S.C.Almo
compound source
Molecule: Programmed Cell Death Protein 1
Chain: A, B
Fragment: Unp Residues 34-150
Synonym: Protein Pd-1
Engineered: Yes
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Pdcd1, Pd1
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 1 Ligand 1
Chain: C
Fragment: Unp Residues 19-239
Synonym: Pd-L1, Pdcd1 Ligand 1, Programmed Death Ligand 1, 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
Expression_system_taxid: 469008
Expression_system_strain: Rosetta (De3) Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-3a
symmetry Space Group: P 21 21 21
R_factor 0.218 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.778 62.843 160.863 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.28 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (154 Kb) [Save to disk]
  • Biological Unit Coordinates (3sbw.pdb1.gz) 110 Kb
  • Biological Unit Coordinates (3sbw.pdb2.gz) 41 Kb
  • CSU: Contacts of Structural Units for 3SBW
  • Structure Factors (406 Kb)
  • Retrieve 3SBW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SBW from S2C, [Save to disk]
  • Re-refined 3sbw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SBW 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 3SBW
  • 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 3SBW, from MSDmotif at EBI
  • Fold representative 3sbw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3sbw_B] [3sbw_A] [3sbw] [3sbw_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3SBW: [IG] [IG_like ] by SMART
  • Other resources with information on 3SBW
  • Community annotation for 3SBW at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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