4NQD Immune System date Nov 25, 2013
title Crystal Structure Of Tcr-Mr1 Ternary Complex And Non-Covalen 5-(2-Oxopropylideneamino)-6-D-Ribitylaminouracil
authors R.W.Birkinshaw, J.Rossjohn
compound source
Molecule: Major Histocompatibility Complex Class I-Related Protein;
Chain: A, C
Synonym: Mhc Class I-Related Gene Protein, Class I Histocom Antigen-Like Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mr1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Beta-2-Microglobulin
Chain: B, F
Synonym: Beta-2-Microglobulin Form Pi 5.3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m, Beta-2 Microglobulin, Cdabp0092, Hdcma22p
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tcr Alpha Chain
Chain: D, G
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Tcr-Alpha
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tcr Beta Chain
Chain: E, H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Tcr-Beta
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.181 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
215.580 68.874 142.977 90.00 104.21 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 2LJ, GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, B
  • cellular response to iron io...

  • Primary referenceT-cell activation by transitory neo-antigens derived from distinct microbial pathways., Corbett AJ, Eckle SB, Birkinshaw RW, Liu L, Patel O, Mahony J, Chen Z, Reantragoon R, Meehan B, Cao H, Williamson NA, Strugnell RA, Van Sinderen D, Mak JY, Fairlie DP, Kjer-Nielsen L, Rossjohn J, McCluskey J, Nature. 2014 Apr 2. doi: 10.1038/nature13160. PMID:24695216
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (272 Kb) [Save to disk]
  • Biological Unit Coordinates (4nqd.pdb1.gz) 67 Kb
  • Biological Unit Coordinates (4nqd.pdb2.gz) 65 Kb
  • Biological Unit Coordinates (4nqd.pdb3.gz) 78 Kb
  • Biological Unit Coordinates (4nqd.pdb4.gz) 74 Kb
  • Biological Unit Coordinates (4nqd.pdb5.gz) 267 Kb
  • LPC: Ligand-Protein Contacts for 4NQD
  • CSU: Contacts of Structural Units for 4NQD
  • Structure Factors (5770 Kb)
  • Retrieve 4NQD in mmCIF format [Save to disk]
  • Re-refined 4nqd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NQD 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 4NQD
  • 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 4NQD, from MSDmotif at EBI
  • Fold representative 4nqd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nqd_A] [4nqd_E] [4nqd_D] [4nqd_F] [4nqd_G] [4nqd_B] [4nqd_H] [4nqd] [4nqd_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4NQD: [IG_like] [IGc1] [IGv ] by SMART
  • Other resources with information on 4NQD
  • Community annotation for 4NQD at PDBWiki (http://pdbwiki.org)

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