7YF5

Crystal Structure of the UDPGA Binding Domain of the Human Phase II Metabolizing Enzyme UDP-Glucuronosyltransferase 2B10

• PDB DOI: https://doi.org/10.2210/pdb7YF5/pdb

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


• Deposited: 2022-07-07 Released: 2023-07-12 
• Deposition Author(s): Yin, X.L., Tong, J.S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.245 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Literature

Crystal Structure Determination of Nucleotide-sugar Binding Domain of Human UDP-glucuronosyltransferases 2B10.

Yin, X., Lu, X., Qi, X., Tu, Y., Zhang, N., Yang, Y., Chen, X., Tong, J.

(2023) Protein Pept Lett 30: 941-950

• PubMed: 37946357 
• DOI: https://doi.org/10.2174/0109298665255492231020050937
• Primary Citation of Related Structures:  
  7YF5


• PubMed Abstract: 
  

  UDP-glucuronosyltransferases (UGTs) play a crucial role in maintaining endobiotic homeostasis and metabolizing xenobiotic compounds, particularly clinical drugs. However, the detailed catalytic mechanism of UGTs has not been fully elucidated due to the limited availability of reliable protein structures. Determining the catalytic domain of human UGTs has proven to be a significant challenge, primarily due to the difficulty in purifying and crystallizing the full-length protein.

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Organizational Affiliation: 

School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 38.36 kDa 
• Atom Count: 2,778 
• Modelled Residue Count: 337 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucuronosyltransferase 2B10	A [auth B], B [auth A]	174	Homo sapiens	Mutation(s): 0  Gene Names: UGT2B10 EC: 2.4.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P36537 (Homo sapiens) Explore P36537  Go to UniProtKB:  P36537
PHAROS:  P36537 GTEx:  ENSG00000109181

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.245 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.907	α = 90
b = 58.387	β = 98.14
c = 68.867	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
autoPROC	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Yin, X.L., Tong, J.S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32101010

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-01-24
  Changes: Database references