1GYK

Serum Amyloid P Component co-crystallised with MOBDG at neutral pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Structures of Crystalline Complexes of Human Serum Amyloid P Component with its Carbohydrate Ligand, the Cyclic Pyruvate Acetal of Galactose

Thompson, D.Pepys, M.B.Tickle, I.Wood, S.P.

(2002) J Mol Biol 320: 1081

  • DOI: https://doi.org/10.1016/s0022-2836(02)00514-4
  • Primary Citation of Related Structures:  
    1GYK

  • PubMed Abstract: 

    Two monoclinic (P2(1)) crystal forms of human serum amyloid P component (SAP) in complex with the 4,6-pyruvate acetal of beta-D-galactose (MObetaDG) were prepared. Structure analysis by molecular replacement and refinement at 2.2A resolution revealed that crystal form 1 (a=95.76A, b=70.53A, c=103.41A, beta=96.80 degrees) contained a pentamer in the asymmetric unit with a structure very similar to that of the published search model. The mode of ligand co-ordination was also similar except that four of the five subunits showed bound ligand with an additional H-bond between O1 of the galactose and the side-chain of Lys79. One sub-unit showed no bound ligand and a vacant calcium site close to a crystal contact. The 2.6A resolution structure of crystal form 2 (a=118.60A, b=109.10A, c=120.80A and beta=95.16 degrees ) showed ten sub-units in the asymmetric unit, all with two bound calcium ions and ligand. The most extensive protein-protein interactions between pentamers describe an AB face-to-face interaction involving 15 ion pairs that sandwiches five molecules of bound MObetaDG at the interface.


  • Organizational Affiliation

    School of Biological Science, University of Southampton, Bassett Crescent East, Hampshire, UK. darren@soton.ac.uk


Macromolecules
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
GTEx:  ENSG00000132703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02743
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDG
Query on CDG

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
N [auth C],
Q [auth D]
METHYL 4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE
C10 H16 O8
ZDZVLEQWFATHTF-IJWOWSJNSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
J [auth B]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
O [auth D],
P [auth D],
R [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.76α = 90
b = 70.53β = 96.8
c = 103.41γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description