8T0S

Crystal structure of UBE2G2 adduct with phenethyl isothiocyanate (PEITC) at the Cys48 position

• PDB DOI: https://doi.org/10.2210/pdb8T0S/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-06-01 Released: 2024-06-05 
• Deposition Author(s): Wang, C., Shaw, G.X., Shi, G., Ji, X.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Crystal structure of UBE2G2 adduct with phenethyl isothiocyanate (PEITC) at the Cys48 position

Wang, C., Shaw, G.X., Shi, G., Ji, X.

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)

Macromolecule Content

• Total Structure Weight: 22.14 kDa 
• Atom Count: 1,837 
• Modelled Residue Count: 190 
• Deposited Residue Count: 192 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 G2	A	165	Homo sapiens	Mutation(s): 2  Gene Names: UBE2G2, UBC7 EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P60604 (Homo sapiens) Explore P60604  Go to UniProtKB:  P60604
PHAROS:  P60604 GTEx:  ENSG00000184787

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase AMFR	B	27	Homo sapiens	Mutation(s): 0  EC: 2.3.2.36
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV5 (Homo sapiens) Explore Q9UKV5  Go to UniProtKB:  Q9UKV5
PHAROS:  Q9UKV5 GTEx:  ENSG00000159461

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
6M6	A	L-PEPTIDE LINKING	C12 H16 N2 O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.894	α = 90
b = 59.345	β = 90
c = 67.901	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Wang, C., Shaw, G.X., Shi, G., Ji, X.

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

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release