3IK5	Viral Protein Signaling Protein	date	Aug 05, 2009
title	Sivmac239 Nef In Complex With Tcr Zeta Itam 1 Polypeptide (A
authors	W.M.Kim, A.B.Sigalov, L.J.Stern
compound		source
Molecule: Protein Nef Chain: A, C Fragment: Core Domain Engineered: Yes		Organism_scientific: Simian Immunodeficiency Virus Organism_common: Siv-Cpz Organism_taxid: 388909 Gene: Nef Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet32a
Molecule: T-Cell Surface Glycoprotein Cd3 Zeta Chain Chain: B, D Fragment: Itam 1 Polypeptide (A63-R80) Synonym: T-Cell Receptor T3 Zeta Chain Engineered: Yes		Synthetic: Yes Other_details: This Sequence Occurs Naturally In Humans.
symmetry	Space Group: P 21 21 21	R_factor 0.170 R_Free 0.184
crystal cell	length a length b length c angle alpha angle beta angle gamma 47.417 47.421 183.520 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.05 Å
subcellular loc.	Membrane localization by OPM: Eukaryotic plasma membrane extracellular side cytoplasmic side
Primary reference	Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments., Kim WM, Sigalov AB, Stern LJ, Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):163-75. Epub 2010 Jan 22. PMID:20124696

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk] Biological Unit Coordinates (3ik5.pdb1.gz) 48 Kb Biological Unit Coordinates (3ik5.pdb2.gz) 25 Kb Biological Unit Coordinates (3ik5.pdb3.gz) 24 Kb CSU: Contacts of Structural Units for 3IK5 Structure Factors (313 Kb) Retrieve 3IK5 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3IK5 from S2C, [Save to disk] Re-refined 3ik5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3IK5 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3IK5

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 3IK5, from MSDmotif at EBI Fold representative 3ik5 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ik5_A] [3ik5_B] [3ik5_C] [3ik5_D] SWISS-PROT database: [Q5QGG3] Domain organization of [Q5QGG3_SIVCZ] by SWISSPFAM Alignments of the sequence of 3IK5 with the sequences similar proteins can be viewed for 3IK5's classification [Q5QGG3_SIVCZ] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [Q5QGG3_SIVCZ] at ProtoMap. Click on the Cluster number.

Other resources with information on 3IK5

Community annotation for 3IK5 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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