3BI9	Immune System	date	Nov 30, 2007
title	Tim-4
authors	C.Santiago, A.Ballesteros, G.G.Kaplan, G.J.Freeman, J.M.Casasnov
compound		source
Molecule: T-Cell Immunoglobulin And Mucin Domain-Containing 4; Chain: X Fragment: N-Terminal Cys-Rich Domain Synonym: Timd-4, T-Cell Membrane Protein 4, Tim-4, Spleen, Containing, Knockout Of Lymphotoxin Protein, Smuckler; Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Strain: Knowles Solter Gene: Timd4, Tim4 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet27b(+)
symmetry	Space Group: P 3 2 1	R_factor 0.236 R_Free 0.268
crystal cell	length a length b length c angle alpha angle beta angle gamma 65.270 65.270 57.020 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.95 Å
ligand	ACT	enzyme
Primary reference	Structures of T Cell Immunoglobulin Mucin Protein 4 Show a Metal-Ion-Dependent Ligand Binding Site where Phosphatidylserine Binds., Santiago C, Ballesteros A, Martinez-Munoz L, Mellado M, Kaplan GG, Freeman GJ, Casasnovas JM, Immunity. 2007 Dec;27(6):941-51. PMID:18083575

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (24 Kb) [Save to disk] Biological Unit Coordinates (3bi9.pdb1.gz) 19 Kb LPC: Ligand-Protein Contacts for 3BI9 CSU: Contacts of Structural Units for 3BI9 Likely Quarternary Molecular Structure file(s) for 3BI9 Structure Factors (157 Kb) Retrieve 3BI9 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3BI9 from S2C, [Save to disk] Re-refined 3bi9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3BI9 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 3BI9

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 3D motif for 3BI9, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3bi9_X] [3bi9] SWISS-PROT database: [Q6U7R4] Domain organization of [TIMD4_MOUSE] by SWISSPFAM Domain found in 3BI9: [IG ] by SMART

Other resources with information on 3BI9

Community annotation for 3BI9 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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