1VDG Immune System date Mar 22, 2004
title Crystal Structure Of Lir1.01, One Of The Alleles Of Lir1
authors M.Shiroishi, L.Rasubala, K.Kuroki, K.Amano, N.Tsuchiya, K.Tokunaga, D.Kohda, K.Maenaka
compound source
Molecule: Leukocyte Immunoglobulin-Like Receptor Subfamily B Member 1;
Chain: A, B
Fragment: Ligand Binding Domain (Domain 1 And 2)
Synonym: Leukocyte Immunoglobulin-Like Receptor 1, Lir-1, Immunoglobulin- Like Transcript 2, Ilt-2, Monocytemacrophage Immunoglobulin-Like Receptor 7, Mir-7, Cd85j Antigen;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgmt7
symmetry Space Group: P 1 21 1
R_factor 0.241 R_Free 0.301
length a length b length c angle alpha angle beta angle gamma
40.969 93.220 57.773 90.00 107.82 90.00
method X-Ray Diffractionresolution 2.80 Å
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1vdg.pdb1.gz) 61 Kb
  • CSU: Contacts of Structural Units for 1VDG
  • Likely Quarternary Molecular Structure file(s) for 1VDG
  • Structure Factors (87 Kb)
  • Retrieve 1VDG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VDG from S2C, [Save to disk]
  • Re-refined 1vdg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VDG 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 1VDG
  • 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 1VDG, from MSDmotif at EBI
  • Fold representative 1vdg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vdg] [1vdg_A] [1vdg_B]
  • SWISS-PROT database: [Q8NHL6]
  • Domain organization of [LIRB1_HUMAN] by SWISSPFAM
  • Domains found in 1VDG: [IG] [IG_like ] by SMART
  • Other resources with information on 1VDG
  • Community annotation for 1VDG 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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