The structure of serum amyloid p component bound to phosphoethanolamine

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

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Ligand Structure Quality Assessment 

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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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serum amyloid P-component
A, B, C, D, E
204Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02743 (Homo sapiens)
Explore P02743 
Go to UniProtKB:  P02743
PHAROS:  P02743
GTEx:  ENSG00000132703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02743
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
Q [auth C],
T [auth D],
X [auth E]
C8 H15 N O6
Query on OPE

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
R [auth D],
V [auth E]
C2 H8 N O4 P
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
I [auth A]
K [auth B]
M [auth B]
O [auth C]
G [auth A],
I [auth A],
K [auth B],
M [auth B],
O [auth C],
P [auth C],
S [auth D],
U [auth D],
W [auth E],
Y [auth E]
Binding Affinity Annotations 
IDSourceBinding Affinity
OPE PDBBind:  3KQR Kd: 3.68e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.86α = 90
b = 69.86β = 96.95
c = 102.27γ = 90
Software Package:
Software NamePurpose
SCALAdata processing
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

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
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary