4ZKB

The chemokine binding protein of orf virus complexed with CCL3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Orf Virus Chemokine Binding Protein in Complex with Host Chemokines Reveal Clues to Broad Binding Specificity.

Counago, R.M.Knapp, K.M.Nakatani, Y.Fleming, S.B.Corbett, M.Wise, L.M.Mercer, A.A.Krause, K.L.

(2015) Structure 23: 1199-1213

  • DOI: 10.1016/j.str.2015.04.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The chemokine binding protein (CKBP) from orf virus (ORFV) binds with high affinity to chemokines from three classes, C, CC, and CXC, making it unique among poxvirus CKBPs described to date. We present its crystal structure alone and in complex with ...

    The chemokine binding protein (CKBP) from orf virus (ORFV) binds with high affinity to chemokines from three classes, C, CC, and CXC, making it unique among poxvirus CKBPs described to date. We present its crystal structure alone and in complex with three CC chemokines, CCL2, CCL3, and CCL7. ORFV CKBP possesses a β-sandwich fold that is electrostatically and sterically complementary to its binding partners. Chemokines bind primarily through interactions involving the N-terminal loop and a hydrophobic recess on the ORFV CKBP β-sheet II surface, and largely polar interactions between the chemokine 20s loop and a negatively charged surface groove located at one end of the CKBP β-sheet II surface. ORFV CKBP interacts with leukocyte receptor and glycosaminoglycan binding sites found on the surface of bound chemokines. SEC-MALLS and chromatographic evidence is presented supporting that ORFV CKBP is a dimer in solution over a broad range of protein concentrations.


    Organizational Affiliation

    Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chemokine binding protein
A
276Orf virusMutation(s): 0 
Find proteins for Q2F862 (Orf virus)
Go to UniProtKB:  Q2F862
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-C motif chemokine 3
B
75Homo sapiensMutation(s): 0 
Gene Names: CCL3 (G0S19-1, MIP1A, SCYA3)
Find proteins for P10147 (Homo sapiens)
Go to Gene View: CCL3
Go to UniProtKB:  P10147
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.268 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.000α = 90.00
b = 78.000β = 90.00
c = 186.020γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-07-15
    Type: Database references
  • Version 1.2: 2018-06-13
    Type: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary