2A3Y

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

Structural Biology Knowledgebase: 2A3Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2A3Y

Classification: Metal Binding Protein

Total Structure Weight: 118995.88

Macromolecule Entities
Molecule Chains Length Organism Details
Serum amyloid P-component A, B, C, D, E 204 Homo sapiens Gene Name(s): APCS Gene View PTX2

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CPJ
Query on CPJ

A, B, C, D, E BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]- 5-YLOXYCARBAMOYL}-ETHANE
C16 H24 N2 O12
HAVIIPIIAVTNFO-GXZHHNFCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C, D, E CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CPJ N/A in BindingDB
IC50: 3800 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.216
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 94.71 α = 90.00
b = 69.96 β = 97.09
c = 101.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-06-27
  • Released Date: 2005-07-26
  • Deposition author(s): Ho, J.G., Kitov, P.I., Paszkiewicz, E., Sadowska, J., Bundle, D.R., Ng, K.K.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4