4AVT

Structure of CPHPC bound to Serum Amyloid P Component


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Interaction of Serum Amyloid P Component with Hexanoyl Bis(D-Proline) (Cphpc)

Kolstoe, S.E.Jenvey, M.C.Purvis, A.Light, M.E.Thompson, D.Hughes, P.Pepys, M.B.Wood, S.P.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2232

  • DOI: 10.1107/S1399004714013455
  • Primary Citation of Related Structures:  
    4AVS, 4AVT, 4AVV, 4AYU

  • PubMed Abstract: 
  • Under physiological conditions, the pentameric human plasma protein serum amyloid P component (SAP) binds hexanoyl bis(D-proline) (R-1-{6-[R-2-carboxy-pyrrolidin-1-yl]-6-oxo-hexanoyl}pyrrolidine-2-carboxylic acid; CPHPC) through its D-proline head groups in a calcium-dependent interaction ...

    Under physiological conditions, the pentameric human plasma protein serum amyloid P component (SAP) binds hexanoyl bis(D-proline) (R-1-{6-[R-2-carboxy-pyrrolidin-1-yl]-6-oxo-hexanoyl}pyrrolidine-2-carboxylic acid; CPHPC) through its D-proline head groups in a calcium-dependent interaction. Cooperative effects in binding lead to a substantial enhancement of affinity. Five molecules of the bivalent ligand cross-link and stabilize pairs of SAP molecules, forming a decameric complex that is rapidly cleared from the circulation by the liver. Here, it is reported that X-ray analysis of the SAP complex with CPHPC and cadmium ions provides higher resolution detail of the interaction than is observed with calcium ions. Conformational isomers of CPHPC observed in solution by HPLC and by X-ray analysis are compared with the protein-bound form. These are discussed in relation to the development of CPHPC to provide SAP depletion for the treatment of amyloidosis and other indications.


    Organizational Affiliation

    Laboratory of Protein Crystallography, Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine (Royal Free Campus), University College London, Rowland Hill Street, London NW3 2PF, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERUM AMYLOID P-COMPONENT
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
204Homo sapiensMutation(s): 0 
Gene Names: APCSPTX2
UniProt & NIH Common Fund Data Resources
Find proteins for P02743 (Homo sapiens)
Explore P02743 
Go to UniProtKB:  P02743
PHAROS:  P02743
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GHE (Subject of Investigation/LOI)
Query on GHE

Download Ideal Coordinates CCD File 
AA [auth E], HA [auth G], P [auth B], RA [auth J], T [auth C](2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid
C16 H24 N2 O6
HZLAWYIBLZNRFZ-VXGBXAGGSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth E] , EA [auth F] , IA [auth G] , LA [auth H] , M [auth A] , OA [auth I] , Q [auth B] , SA [auth J] , 
BA [auth E], EA [auth F], IA [auth G], LA [auth H], M [auth A], OA [auth I], Q [auth B], SA [auth J], U [auth C], X [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth F] , DA [auth F] , FA [auth G] , GA [auth G] , JA [auth H] , K [auth A] , KA [auth H] , L [auth A] , 
CA [auth F], DA [auth F], FA [auth G], GA [auth G], JA [auth H], K [auth A], KA [auth H], L [auth A], MA [auth I], N [auth B], NA [auth I], O [auth B], PA [auth J], QA [auth J], R [auth C], S [auth C], V [auth D], W [auth D], Y [auth E], Z [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 230.864α = 90
b = 230.864β = 90
c = 281.393γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2014-08-06
    Changes: Database references
  • Version 1.2: 2014-10-22
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary