5TR4 | pdb_00005tr4

Structure of Ubiquitin activating enzyme (Uba1) in complex with ubiquitin and TAK-243

• PDB DOI: https://doi.org/10.2210/pdb5TR4/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Saccharomyces cerevisiae S288C, Bos taurus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-10-25 Released: 2017-11-01 
• Deposition Author(s): Sintchak, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.256 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Identification and Characterization of a Small Molecule Inhibitor of the Ubiquitin Activating Enzyme (TAK-243)

Hyer, M., Milhollen, M., Ciavarri, J., Fleming, P., Traore, T., Sappal, D., Huck, J., Shi, J., Gavin, J., Brownell, J., Yang, Y., Stringer, B., Griffin, R., Bruzzese, F., Soucy, T., Duffy, J., Rabino, C., Riceberg, J., Hoar, K., Lublinsky, A., Menon, S., Sintchak, M., Bump, N., Pulukuri, S., Amidon, B., Langston, S., Tirrell, S., Kuranda, M., Veiby, P., Newcomb, J., Li, P., Wu, J., Dick, L., Greenspan, P., Galvin, K., Manfredi, M., Claibrone, C., Bence, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 245.59 kDa 
• Atom Count: 16,349 
• Modeled Residue Count: 2,075 
• Deposited Residue Count: 2,186 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-activating enzyme E1 1	A, C	1,017	Saccharomyces cerevisiae S288C	Mutation(s): 2  Gene Names: UBA1, YKL210W EC: 6.2.1.45
UniProt
Find proteins for P22515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22515  Go to UniProtKB:  P22515

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B, D	76	Bos taurus	Mutation(s): 0  Gene Names: UBB
UniProt
Find proteins for P0CG53 (Bos taurus) Explore P0CG53  Go to UniProtKB:  P0CG53

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
61T	E [auth B], F [auth D]	[(1~{R},2~{R},3~{S},4~{R})-2,3-bis(oxidanyl)-4-[[2-[3-(trifluoromethylsulfanyl)phenyl]pyrazolo[1,5-a]pyrimidin-7-yl]amino]cyclopentyl]methyl sulfamate C19 H20 F3 N5 O5 S2 KJDAGXLMHXUAGV-DGWLBADLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.256 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.485	α = 90
b = 172.148	β = 90
c = 79.424	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing
HKL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Sintchak, M.D.

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary