3KQR

The structure of serum amyloid p component bound to phosphoethanolamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.141 

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:  

  • 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 pr ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serum amyloid P-component
A, B, C, D, E
204Homo sapiensMutation(s): 0 
Gene Names: APCS (PTX2)
Find proteins for P02743 (Homo sapiens)
Go to Gene View: APCS
Go to UniProtKB:  P02743
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OPE
Query on OPE

Download SDF File 
Download CCD File 
A, B, C, D, E
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER
COLAMINE PHOSPHORIC ACID
C2 H8 N O4 P
SUHOOTKUPISOBE-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OPEKd: 36800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.860α = 90.00
b = 69.860β = 96.95
c = 102.270γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata processing
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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