4E4C | pdb_00004e4c

Crystal structure of Notexin at 1.8 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4E4C/pdb

• Classification: HYDROLASE
• Organism(s): Notechis scutatus scutatus
• Mutation(s): No 


• Deposited: 2012-03-12 Released: 2012-03-28 
• Deposition Author(s): Ullah, A., Spencer, P., Murakami, M.T., Arni, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.322 (Depositor), 0.318 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.266 (Depositor) 

Starting Model: experimental

Literature

High resolution structure of Notexin

Ullah, A., Spencer, P., Murakami, M.T., Arni, R.K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14 kDa 
• Atom Count: 1,044 
• Modeled Residue Count: 118 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2	A	119	Notechis scutatus scutatus	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P00608 (Notechis scutatus scutatus) Explore P00608  Go to UniProtKB:  P00608

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.322 (Depositor), 0.318 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.266 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.1	α = 90
b = 74.1	β = 90
c = 48.738	γ = 120

Software Package:

Software Name	Purpose
NatXray	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Ullah, A., Spencer, P., Murakami, M.T., Arni, R.K.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary