Decameric structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2-carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history



Ho, J.G.Kitov, P.I.Paszkiewicz, E.Sadowska, J.Bundle, D.R.Ng, K.K.

(2005) J Biol Chem 280: 31999-32008

  • DOI: https://doi.org/10.1074/jbc.M504403200
  • Primary Citation of Related Structures:  
    2A3W, 2A3X, 2A3Y

  • PubMed Abstract: 

    A comprehensive series of solution and crystallographic studies reveal how simple, achiral, bivalent ligands of the cyclic pyruvate of glycerol promote face-to-face complex formation of the pentraxin, serum amyloid P component (SAP) into decamers. SAP, a protein of the human innate immune system, is universally present in amyloids, including cerebral amyloid deposits found in the brain of Alzheimer disease patients. Removal of SAP through a specific aggregation mechanism mediated by multivalent ligands appears to provide therapeutic benefit in the progression of this disease. Crystallographic studies reveal that in our novel series of ligands only the methyl and carboxylate moieties of the pyruvate ketal directly interact with the protein, but the geometric constraints imposed by the tether dictate which of two chair conformations are adopted by the pyruvate dioxane ring. Solution studies, as interpreted through a simple thermodynamic model, account for the distribution of pentameric and decameric bound states at different ligand concentrations and indicate that differences in the flexibility of the tether determine the geometry and stability of the specific aggregates formed between SAP and two different bivalent ligands. The factors affecting the design of ligands promoting face-to-face protein dimerization as well as potential biological implications are discussed.

  • Organizational Affiliation

    Department of Biological Sciences, University of Calgary, Alberta, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serum amyloid P-component
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
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CPJ

Download Ideal Coordinates CCD File 
AB [auth M]
CA [auth C]
DB [auth N]
FA [auth D]
IA [auth E]
AB [auth M],
CA [auth C],
DB [auth N],
FA [auth D],
IA [auth E],
IB [auth P],
LB [auth Q],
W [auth A],
XA [auth L],
Z [auth B]
C16 H24 N2 O12
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
BB [auth N]
CB [auth N]
DA [auth D]
AA [auth C],
BA [auth C],
BB [auth N],
CB [auth N],
DA [auth D],
EA [auth D],
EB [auth O],
FB [auth O],
GA [auth E],
GB [auth P],
HA [auth E],
HB [auth P],
JA [auth F],
JB [auth Q],
KA [auth F],
KB [auth Q],
LA [auth G],
MA [auth G],
MB [auth R],
NA [auth H],
NB [auth R],
OA [auth H],
OB [auth S],
PA [auth I],
PB [auth S],
QA [auth I],
QB [auth T],
RA [auth J],
RB [auth T],
SA [auth J],
TA [auth K],
U [auth A],
UA [auth K],
V [auth A],
VA [auth L],
WA [auth L],
X [auth B],
Y [auth B],
YA [auth M],
ZA [auth M]
Binding Affinity Annotations 
IDSourceBinding Affinity
CPJ PDBBind:  2A3W IC50: 3800 (nM) from 1 assay(s)
Binding MOAD:  2A3W IC50: 3800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.712α = 86.53
b = 105.325β = 78.15
c = 146.007γ = 76.78
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2020-01-22
    Changes: Advisory, Derived calculations
  • Version 1.5: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description