3ODU Signaling Protein, Hydrolase date Aug 11, 2010
title The 2.5 A Structure Of The Cxcr4 Chemokine Receptor In Compl Small Molecule Antagonist It1t
authors B.Wu, C.D.Mol, G.W.Han, V.Katritch, E.Y.T.Chien, W.Liu, V.Cherezov R.C.Stevens, Accelerated Technologies Center For Gene To 3d (Atcg3d), Gpcr Network (Gpcr)
compound source
Molecule: C-X-C Chemokine Receptor Type 4, Lysozyme Chimera
Chain: A, B
Fragment: Cxcr4 Residues 2-229, Lysozyme Residues 1002-1161 Residues 230-319;
Synonym: Cxc-R4, Cxcr-4, Stromal Cell-Derived Factor 1 Rece Receptor, Fusin, Leukocyte-Derived Seven Transmembrane Do Receptor, Lestr, Lcr1, Fb22, Npyrl, Hm89, Lysis Protein, Mu Endolysin;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens, Enterobacteria Phage T4
Organism_taxid: 9606, 10665
Gene: Cxcr4, Cxcr4_human, E
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Bacmid
Expression_system_plasmid: Pfastbac
symmetry Space Group: P 1 21 1
R_factor 0.237 R_Free 0.282
length a length b length c angle alpha angle beta angle gamma
64.540 83.692 119.995 90.00 102.17 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand ITD, OLA, OLC BindingDB enzyme Hydrolase E.C. BRENDA
Gene CXCR4 (H. sapiens)
A, B

Disease Myelokathexis, isolated OMIM:162643
WHIM syndrome OMIM:162643
Primary referenceStructures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists., Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC, Science. 2010 Oct 7. PMID:20929726
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (323 Kb) [Save to disk]
  • Biological Unit Coordinates (3odu.pdb1.gz) 314 Kb
  • LPC: Ligand-Protein Contacts for 3ODU
  • CSU: Contacts of Structural Units for 3ODU
  • Structure Factors (885 Kb)
  • Retrieve 3ODU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ODU from S2C, [Save to disk]
  • Re-refined 3odu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ODU 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 3ODU
  • 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 3ODU, from MSDmotif at EBI
  • Fold representative 3odu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3odu_B] [3odu] [3odu_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3ODU
  • Community annotation for 3ODU 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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