8IND

Crystal structure of UGT74AN3-UDP-RES

• PDB DOI: https://doi.org/10.2210/pdb8IND/pdb

• Classification: TRANSFERASE
• Organism(s): Catharanthus roseus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-09 Released: 2024-01-24 
• Deposition Author(s): Huang, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.216 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Substrate Promiscuity, Crystal Structure, and Application of a Plant UDP-Glycosyltransferase UGT74AN3

Huang, W., Zhang, X., Li, J., Lv, J., Wang, Y., He, Y., Song, J., Agren, H., Jiang, R., Deng, Z., Long, F.

(2024) ACS Catal 14: 475-488

• DOI: https://doi.org/10.1021/acscatal.3c05309

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: 53.59 kDa 
• Atom Count: 3,700 
• Modelled Residue Count: 427 
• Deposited Residue Count: 465 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	465	Catharanthus roseus	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for W8JMV4 (Catharanthus roseus) Explore W8JMV4  Go to UniProtKB:  W8JMV4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	C [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
6JI	B [auth A]	5-[(1R,2S,4R,6R,7R,10S,11S,14S,16R)-14-hydroxy-7,11-dimethyl-3-oxapentacyclo[8.8.0.02,4.02,7.011,16]octadecan-6-yl]pyran-2-one C24 H32 O4 ATLJNLYIJOCWJE-CWMZOUAVSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.216 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.995	α = 90
b = 52.911	β = 90
c = 201.119	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
XDS	data reduction
Aimless	data scaling
PHENIX	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Huang, W.

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

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release