5TSF | pdb_00005tsf

Crystal structure of AChBP from Aplysia californica complex with 2-aminopyrimidine at pH 7.0 spacegroup P212121

• PDB DOI: https://doi.org/10.2210/pdb5TSF/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Aplysia californica
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-10-28 Released: 2017-10-25 
• Deposition Author(s): Camacho-Hernandez, G.A., Kaczanowska, K., Harel, M., Finn, M.G., Taylor, P.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AChBP from Aplysia californica complex with 2-aminopyrimidine at pH 7.0 spacegroup P212121

Camacho-Hernandez, G.A., Kaczanowska, K., Harel, M., Finn, M.G., Taylor, P.W.

To be published.

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: 133.14 kDa 
• Atom Count: 9,107 
• Modeled Residue Count: 1,063 
• Deposited Residue Count: 1,150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble acetylcholine receptor	A, B, C, D, E	230	Aplysia californica	Mutation(s): 0
UniProt
Find proteins for Q8WSF8 (Aplysia californica) Explore Q8WSF8  Go to UniProtKB:  Q8WSF8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7KO	F [auth A], G [auth A], J [auth C], K [auth D], L [auth E]	6-chloro-N~4~,N~4~-bis[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine C16 H15 Cl N6 JDMRUOFJLDXEIQ-UHFFFAOYSA-N
NAG	H [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.19	α = 90
b = 115.7	β = 90
c = 131	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Camacho-Hernandez, G.A., Kaczanowska, K., Harel, M., Finn, M.G., Taylor, P.W.

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2021-03-24
  Changes: Source and taxonomy, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary