1I7L | pdb_00001i7l

CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX OF THE C DOMAIN OF SYNAPSIN II FROM RAT WITH ATP

• PDB DOI: https://doi.org/10.2210/pdb1I7L/pdb

• Classification: NEUROPEPTIDE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-03-09 Released: 2003-07-01 
• Deposition Author(s): Esser, L., Palnitkar, M., Deisenhofer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.289 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.210 (DCC) 

Literature

ATP Binding Independent of Metal Cations in Synapsin II

Esser, L., Palnitkar, M., Deisenhofer, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.18 kDa 
• Atom Count: 5,181 
• Modeled Residue Count: 618 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNAPSIN II	A, B	309	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q63537 (Rattus norvegicus) Explore Q63537  Go to UniProtKB:  Q63537

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A], D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.289 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.210 (DCC) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.275	α = 90
b = 121.275	β = 90
c = 165.891	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-01 
Deposition Author(s): Esser, L., Palnitkar, M., Deisenhofer, J.

Revision History  

• Version 1.0: 2003-07-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations