7TBA

Pentraxin - ligand complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A novel phosphocholine-mimetic inhibits a pro-inflammatory conformational change in C-reactive protein.

Zeller, J.Cheung Tung Shing, K.S.Nero, T.L.McFadyen, J.D.Krippner, G.Bogner, B.Kreuzaler, S.Kiefer, J.Horner, V.K.Braig, D.Danish, H.Baratchi, S.Fricke, M.Wang, X.Kather, M.G.Kammerer, B.Woollard, K.J.Sharma, P.Morton, C.J.Pietersz, G.Parker, M.W.Peter, K.Eisenhardt, S.U.

(2023) EMBO Mol Med 15: e16236-e16236

  • DOI: https://doi.org/10.15252/emmm.202216236
  • Primary Citation of Related Structures:  
    7TBA

  • PubMed Abstract: 

    C-reactive protein (CRP) is an early-stage acute phase protein and highly upregulated in response to inflammatory reactions. We recently identified a novel mechanism that leads to a conformational change from the native, functionally relatively inert, pentameric CRP (pCRP) structure to a pentameric CRP intermediate (pCRP*) and ultimately to the monomeric CRP (mCRP) form, both exhibiting highly pro-inflammatory effects. This transition in the inflammatory profile of CRP is mediated by binding of pCRP to activated/damaged cell membranes via exposed phosphocholine lipid head groups. We designed a tool compound as a low molecular weight CRP inhibitor using the structure of phosphocholine as a template. X-ray crystallography revealed specific binding to the phosphocholine binding pockets of pCRP. We provide in vitro and in vivo proof-of-concept data demonstrating that the low molecular weight tool compound inhibits CRP-driven exacerbation of local inflammatory responses, while potentially preserving pathogen-defense functions of CRP. The inhibition of the conformational change generating pro-inflammatory CRP isoforms via phosphocholine-mimicking compounds represents a promising, potentially broadly applicable anti-inflammatory therapy.


  • Organizational Affiliation

    Department of Plastic and Hand Surgery, University of Freiburg Medical Centre, Medical Faculty of the University of Freiburg, Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-reactive protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
206Homo sapiensMutation(s): 0 
Gene Names: CRPPTX1
UniProt & NIH Common Fund Data Resources
Find proteins for P02741 (Homo sapiens)
Explore P02741 
Go to UniProtKB:  P02741
PHAROS:  P02741
GTEx:  ENSG00000132693 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02741
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XQY (Subject of Investigation/LOI)
Query on XQY

Download Ideal Coordinates CCD File 
AA [auth C]
BB [auth L]
DA [auth D]
EB [auth M]
GA [auth E]
AA [auth C],
BB [auth L],
DA [auth D],
EB [auth M],
GA [auth E],
HB [auth N],
JA [auth F],
KB [auth O],
MA [auth G],
NB [auth P],
PA [auth H],
QB [auth Q],
SA [auth I],
TB [auth R],
U [auth A],
VA [auth J],
WB [auth S],
X [auth B],
YA [auth K],
ZB [auth T]
[3-(dibutylamino)propyl]phosphonic acid
C11 H26 N O3 P
XATRQYYMOIGUKL-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth K]
AC [auth T]
BA [auth C]
BC [auth T]
CA [auth C]
AB [auth K],
AC [auth T],
BA [auth C],
BC [auth T],
CA [auth C],
CB [auth L],
DB [auth L],
EA [auth D],
FA [auth D],
FB [auth M],
GB [auth M],
HA [auth E],
IA [auth E],
IB [auth N],
JB [auth N],
KA [auth F],
LA [auth F],
LB [auth O],
MB [auth O],
NA [auth G],
OA [auth G],
OB [auth P],
PB [auth P],
QA [auth H],
RA [auth H],
RB [auth Q],
SB [auth Q],
TA [auth I],
UA [auth I],
UB [auth R],
V [auth A],
VB [auth R],
W [auth A],
WA [auth J],
XA [auth J],
XB [auth S],
Y [auth B],
YB [auth S],
Z [auth B],
ZA [auth K]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.568α = 89.08
b = 98.172β = 89.76
c = 160.4γ = 87.48
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references, Refinement description
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description