5LNB | pdb_00005lnb

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.197 (Depositor), 0.200 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the de-sumoylating protease

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40537
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.197 (Depositor), 0.200 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.161 (Depositor)

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.