6DHB Immune System date May 19, 2018
title Crystal Structure Of The Human Tim-3 With Bound Calcium
authors A.K.Gandhi, W.M.Kim, Y.H.Huang, D.Bonsor, E.Sundberg, Z.Y.Sun, G. V.Kuchroo, R.S.Blumberg
compound source
Molecule: Hepatitis A Virus Cellular Receptor 2
Chain: A
Fragment: Unp Residues 24-130
Synonym: Havcr-2,T-Cell Immunoglobulin And Mucin Domain-Con Protein 3,Timd-3,T-Cell Immunoglobulin Mucin Receptor 3,Tim Membrane Protein 3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Havcr2, Tim3, Timd3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.150 R_Free 0.181
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.310 43.060 51.720 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand BEZ, CA, EDO enzyme
Primary referenceHigh resolution X-ray and NMR structural study of human T-cell immunoglobulin and mucin domain containing protein-3., Gandhi AK, Kim WM, Sun ZJ, Huang YH, Bonsor DA, Sundberg EJ, Kondo Y, Wagner G, Kuchroo VK, Petsko G, Blumberg RS, Sci Rep. 2018 Nov 30;8(1):17512. doi: 10.1038/s41598-018-35754-0. PMID:30504845
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (25 Kb) [Save to disk]
  • Biological Unit Coordinates (6dhb.pdb1.gz) 20 Kb
  • LPC: Ligand-Protein Contacts for 6DHB
  • CSU: Contacts of Structural Units for 6DHB
  • Structure Factors (473 Kb)
  • Retrieve 6DHB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6DHB from S2C, [Save to disk]
  • View 6DHB 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 6DHB
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6dhb_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6DHB
  • Community annotation for 6DHB at PDBWiki (http://pdbwiki.org)

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