1SAC

THE STRUCTURE OF PENTAMERIC HUMAN SERUM AMYLOID P COMPONENT

• PDB DOI: https://doi.org/10.2210/pdb1SAC/pdb

• Classification: AMYLOID PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1994-01-27 Released: 1994-05-31 
• Deposition Author(s): White, H.E., Emsley, J., O'Hara, B.P., Oliva, G., Srinivasan, N., Tickle, I.J., Blundell, T.L., Pepys, M.B., Wood, S.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Literature

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: 338-345

• PubMed: 8114934 
• DOI: https://doi.org/10.1038/367338a0
• Primary Citation of Related Structures:  
  1SAC


• PubMed Abstract: 
  

  The three-dimensional structure of pentameric human serum amyloid P component at high resolution, the first reported for a pentraxin, reveals that the tertiary fold is remarkably similar to that of the legume lectins. Carboxylate and phosphate compounds bind directly to two calcium ions; interactions with a carboxyethylidene ring are mediated by Asn 59 and Gln 148 ligands of the calcium ions. These X-ray results indicate the probable modes of binding of the biologically important ligands, DNA and amyloid fibrils.

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Organizational Affiliation: 

Laboratory of Molecular Biology, Birkbeck College, London, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.05 kDa 
• Atom Count: 8,271 
• Modelled Residue Count: 1,020 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERUM AMYLOID P COMPONENT	A, B, C, D, E	204	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02743 (Homo sapiens) Explore P02743  Go to UniProtKB:  P02743
PHAROS:  P02743 GTEx:  ENSG00000132703

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	H [auth A], K [auth B], P [auth D], S [auth E]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], N [auth D], O [auth D], Q [auth E], R [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.9	α = 90
b = 99.3	β = 95.9
c = 96.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
RESTRAIN	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-05-31 
Deposition Author(s): White, H.E., Emsley, J., O'Hara, B.P., Oliva, G., Srinivasan, N., Tickle, I.J., Blundell, T.L., Pepys, M.B., Wood, S.P.

Revision History  

• Version 1.0: 1994-05-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary