5LNB

Crystal structure of the de-sumoylating protease

• PDB DOI: https://doi.org/10.2210/pdb5LNB/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-03 Released: 2017-08-16 
• Deposition Author(s): Eckhoff, J., Dohmen, J., Pichlo, C., Baumann, U.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.197 
• R-Value Work: 0.157 
• R-Value Observed: 0.161 

Literature

Crystal structure of the de-sumoylating protease

Eckhoff, J., Dohmen, J., Pichlo, C., Baumann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.67 kDa 
• Atom Count: 2,377 
• Modelled Residue Count: 259 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like-specific protease 2	A [auth B]	310	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: ULP2, SMT4, YIL031W EC: 3.4.22.68 (PDB Primary Data), 3.4.22 (UniProt)
UniProt
Find proteins for P40537 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40537  Go to UniProtKB:  P40537

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.197 
• R-Value Work: 0.157 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.54	α = 90
b = 55.58	β = 90
c = 172.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Eckhoff, J., Dohmen, J., Pichlo, C., Baumann, U.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references