7TUO | pdb_00007tuo

Crystal structure analysis of human USP28 complex with a compound

• PDB DOI: https://doi.org/10.2210/pdb7TUO/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-02-03 Released: 2023-02-15 
• Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of human USP28 complex with a compound

Seo, H.-S., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.85 kDa 
• Atom Count: 2,896 
• Modeled Residue Count: 320 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 28	A	385	Homo sapiens	Mutation(s): 0  Gene Names: USP28, KIAA1515 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RU2 (Homo sapiens) Explore Q96RU2  Go to UniProtKB:  Q96RU2
PHAROS:  Q96RU2 GTEx:  ENSG00000048028

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KL9 (Subject of Investigation/LOI)	B [auth A], C [auth A]	7-amino-N-(2-{4-[(1R,3s,5S)-8-azabicyclo[3.2.1]octan-3-yl]phenyl}ethyl)-3-methylthieno[2,3-b]pyrazine-6-carboxamide C23 H27 N5 O S HYCWFJHZOMDKSR-NNZMDNLPSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.64	α = 90
b = 114.64	β = 90
c = 114.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description