3D2U Immune System date May 08, 2008
title Structure Of Ul18, A Peptide-Binding Viral Mhc Mimic, Bound Inhibitory Receptor
authors Z.Yang, P.J.Bjorkman
compound source
Molecule: Ul18 Protein
Chain: A, E
Fragment: Sequence Database Residues 21-301
Organism_scientific: Human Herpesvirus 5
Organism_common: Human Cytomegalovirus
Organism_taxid: 10359
Strain: Ad169
Other_details: Gene Ul18

Molecule: Beta-2-Microglobulin
Chain: B, F

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Beta2m

Molecule: Leukocyte Immunoglobulin-Like Receptor Subfamily 1;
Chain: D, H
Fragment: Ig-Like C2-Type 1 And C2-Type 2 Domains
Synonym: Leukocyte Immunoglobulin-Like Receptor 1, Lir-1, Immunoglobulin- Like Transcript 2, Ilt-2, Monocytemacropha Immunoglobulin-Like Receptor 7, Mir-7, Cd85j Antigen;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Lir-1

Molecule: Actin
Chain: G, C
Fragment: Sequence Database Residues 170-178
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.241 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.366 98.110 172.147 90.00 98.46 90.00
method X-Ray Diffractionresolution 2.21 Å
ligand BMA, FUC, MAN, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, B
  • cellular response to iron io...

  • Primary referenceStructure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor., Yang Z, Bjorkman PJ, Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):10095-100. Epub 2008 Jul 15. PMID:18632577
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (200 Kb) [Save to disk]
  • Biological Unit Coordinates (3d2u.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (3d2u.pdb2.gz) 99 Kb
  • LPC: Ligand-Protein Contacts for 3D2U
  • CSU: Contacts of Structural Units for 3D2U
  • Likely Quarternary Molecular Structure file(s) for 3D2U
  • Structure Factors (1373 Kb)
  • Retrieve 3D2U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D2U from S2C, [Save to disk]
  • Re-refined 3d2u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D2U 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 3D2U
  • 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 3D2U, from MSDmotif at EBI
  • Fold representative 3d2u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d2u] [3d2u_D] [3d2u_B] [3d2u_H] [3d2u_E] [3d2u_C] [3d2u_G] [3d2u_A] [3d2u_F]
  • SWISS-PROT database: [P60709] [P61769] [Q8NHL6] [P08560]
  • Domain organization of [ACTB_HUMAN] [B2MG_HUMAN] [LIRB1_HUMAN] [VGH3_HCMVA] by SWISSPFAM
  • Domains found in 3D2U: [IG] [IG_like] [IGc1 ] by SMART
  • Other resources with information on 3D2U
  • Community annotation for 3D2U at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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