5TYT Protein Binding date Nov 21, 2016
title Crystal Structure Of The Pdz Domain Of Rhogef Bound To Cxcr2 Terminal Peptide
authors N.Spellmon, J.Holcomb, A.Niu, V.Choudhary, X.Sun, J.Brunzelle, C.L
compound source
Molecule: Rho Guanine Nucleotide Exchange Factor 11, C-X-C Receptor Type 2 Chimera;
Chain: A, B, C, D
Fragment: Rho (Unp Residues 41-123), Cxcr2 C-Terminal Pepti Residues 356-360);
Synonym: Pdz-Rhogef,Cxcr-2, Cdw128b, Gromgsa Receptor, Hig Interleukin-8 Receptor B, Il-8r B, Il-8 Receptor Type 2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Arhgef11, Kiaa0380, Cxcr2, Il8rb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdf-Sumo
symmetry Space Group: C 2 2 21
R_factor 0.207 R_Free 0.240
length a length b length c angle alpha angle beta angle gamma
61.739 66.633 168.440 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
A, D, C, B

Primary referenceStructural basis of PDZ-mediated chemokine receptor CXCR2 scaffolding by guanine nucleotide exchange factor PDZ-RhoGEF., Spellmon N, Holcomb J, Niu A, Choudhary V, Sun X, Zhang Y, Wan J, Doughan M, Hayden S, Hachem F, Brunzelle J, Li C, Yang Z, Biochem Biophys Res Commun. 2017 Apr 1;485(2):529-534. doi:, 10.1016/j.bbrc.2017.02.010. Epub 2017 Feb 6. PMID:28179147
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (5tyt.pdb1.gz) 56 Kb
  • Biological Unit Coordinates (5tyt.pdb2.gz) 57 Kb
  • CSU: Contacts of Structural Units for 5TYT
  • Structure Factors (566 Kb)
  • Retrieve 5TYT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TYT from S2C, [Save to disk]
  • Re-refined 5tyt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5TYT 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 5TYT
  • 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
  • Fold representative 5tyt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5tyt_A] [5tyt_D] [5tyt] [5tyt_C] [5tyt_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5TYT
  • Community annotation for 5TYT at PDBWiki (http://pdbwiki.org)

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