8INO | pdb_00008ino

Crystal structure of UGT74AN3 in complex UDP and PER

• PDB DOI: https://doi.org/10.2210/pdb8INO/pdb

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


• Deposited: 2023-03-10 Released: 2024-01-24 
• Deposition Author(s): Long, F., Huang, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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: 53.46 kDa 
• Atom Count: 3,485 
• Modeled Residue Count: 421 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	464	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	C [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
Q30	B [auth A]	3-[(3S,5S,8S,9S,10R,13R,14S,17R)-10,13-dimethyl-3,5,14-tris(oxidanyl)-2,3,4,6,7,8,9,11,12,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-17-yl]-2H-furan-5-one C23 H34 O5 QJPCKAJTLHDNCS-STPRYWCXSA-N
TRS (Subject of Investigation/LOI)	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: 2.30 Å
• R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.608	α = 90
b = 52.2	β = 90
c = 200.701	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

---

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

Revision History  

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