3L2Y

The structure of C-reactive protein bound to phosphoethanolamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of ligand specificity in the human pentraxins, C-reactive protein and serum amyloid P component.

Mikolajek, H.Kolstoe, S.E.Pye, V.E.Mangione, P.Pepys, M.B.Wood, S.P.

(2011) J Mol Recognit 24: 371-377

  • DOI: 10.1002/jmr.1090
  • Primary Citation of Related Structures:  
    3KQR, 3L2Y

  • PubMed Abstract: 
  • The normal physiological roles of the phylogenetically conserved human plasma proteins C-reactive protein (CRP) and serum amyloid P component (SAP) are not known. Novel drugs targeting their ligand specificities are in clinical development as both proteins have significant pathophysiological effects, SAP in promoting amyloidosis and CRP in exacerbating ischemic injury ...

    The normal physiological roles of the phylogenetically conserved human plasma proteins C-reactive protein (CRP) and serum amyloid P component (SAP) are not known. Novel drugs targeting their ligand specificities are in clinical development as both proteins have significant pathophysiological effects, SAP in promoting amyloidosis and CRP in exacerbating ischemic injury. Both proteins bind to phosphoethanolamine and we show here that, under physiological conditions, phosphoethanolamine is bound with higher affinity by human SAP than by human CRP. An explanation is provided by X-ray crystal structures that show SAP residue Tyr74 allowing additional hydrophobic protein-ligand interactions compared with the equivalent Thr76 of CRP. Docking simulations show many more low energy positions for phosphoethanolamine bound by CRP than by SAP and are consistent with the crystallographic and functional binding results. These fundamental observations on structure-activity relationships will aid the design of improved pentraxin targeting drugs.


    Organizational Affiliation

    Laboratory of Protein Crystallography, Acute Phase Proteins, Division of Medicine, Royal Free Campus, University College London Medical School, Rowland Hill Street, London NW3 2PF, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-reactive protein
A, B, C, D, E, F, G, H
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OPE
Query on OPE

Download Ideal Coordinates CCD File 
AA [auth C] , BB [auth L] , DA [auth D] , EB [auth M] , GA [auth E] , HB [auth N] , JA [auth F] , KB [auth O] , 
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],  VA [auth J],  W [auth A],  WB [auth S],  X [auth B],  YA [auth K],  ZB [auth T]
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER
C2 H8 N O4 P
SUHOOTKUPISOBE-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth K] , AC [auth T] , BA [auth C] , BC [auth T] , CA [auth C] , CB [auth L] , DB [auth L] , EA [auth D] , 
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],  U [auth A],  UA [auth I],  UB [auth R],  V [auth A],  VB [auth R],  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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
OPE PDBBind:  3L2Y Kd: 3.21e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 278.448α = 90
b = 278.448β = 90
c = 92.111γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance