8T0S | pdb_00008t0s

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.208 (Depositor), 0.208 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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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.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60604
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UKV5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
6M6 Query on 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 (Depositor), 0.208 (DCC)
R-Value Work: 0.174 (Depositor), 0.174 (DCC)
R-Value Observed: 0.176 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-05

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.