1LGN

DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP.

Hohenester, E.Hutchinson, W.L.Pepys, M.B.Wood, S.P.

(1997) J.Mol.Biol. 269: 570-578

  • DOI: 10.1006/jmbi.1997.1075

  • PubMed Abstract: 
  • Serum amyloid P component (SAP) is a glycoprotein that binds in a calcium-dependent fashion to a variety of ligands including other proteins, glycosaminoglycans and DNA. SAP is universally associated with the amyloid deposits in all forms of amyloido ...

    Serum amyloid P component (SAP) is a glycoprotein that binds in a calcium-dependent fashion to a variety of ligands including other proteins, glycosaminoglycans and DNA. SAP is universally associated with the amyloid deposits in all forms of amyloidoses including Alzheimer's disease. Small-molecule ligands that displace SAP from amyloid fibrils and thereby expose the fibrils to proteolytic clearance mechanisms hold potential as drugs for the prevention and treatment of amyloidosis. We have carried out a screen for novel SAP ligands and have identified 2'-deoxyadenosine-5'-monophosphate (dAMP) as a ligand. The crystal structure of the SAP-dAMP complex determined at 2.8 A resolution (R = 0.232, R(free) = 0.252) reveals a decamer in which all interactions between SAP pentamers are mediated by the ligand. The stability of the decamer in solution has been demonstrated by gel filtration chromatography. The two calcium ions of SAP are bridged by the dAMP phosphate group and five hydrogen bonds are formed between the protein and the ligand, including specific interactions made by the adenine base. This mode of dAMP binding is not compatible with the nucleotide being part of double-helical DNA. The SAP-dAMP decamer is stabilized mainly by base-stacking of adjacent ligand molecules and possibly by electrostatic interactions involving the dAMP phosphate groups; decamerization buries 1000 A2 (2.6%) of the pentamer solvent-accessible surface. Ligand-induced decamerization of SAP, which utilizes the high cooperativity of a multiple-site interaction, may be a strategy to overcome the problems for drug design associated with the rather modest affinities of SAP for small-molecule ligands.


    Related Citations: 
    • Structure of Pentameric Human Serum Amyloid P Component
      Emsley, J.,White, H.E.,O'Hara, B.P.,Oliva, G.,Srinivasan, N.,Tickle, I.J.,Blundell, T.L.,Pepys, M.B.,Wood, S.P.
      (1994) Nature 367: 338


    Organizational Affiliation

    Department of Crystallography, Birkbeck College, University of London, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Download SDF File 
Download CCD File 
A, B, C, D, E
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.232 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 190.030α = 90.00
b = 190.030β = 90.00
c = 119.740γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
MOSFLMdata reduction
CCP4data reduction
X-PLORrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-24
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance