8INA | pdb_00008ina

Crystal structure of UGT74AN3-UDP

PDB DOI: https://doi.org/10.2210/pdb8INA/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): Long, F., Huang, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.221 (Depositor), 0.221 (DCC)
R-Value Work:
0.187 (Depositor), 0.186 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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

Macromolecule Content

Total Structure Weight: 54.07 kDa
Atom Count: 3,689
Modeled Residue Count: 431
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	474	Catharanthus roseus	Mutation(s): 0 EC: 2.4.1
UniProt
Find proteins for W8JMV4 (Catharanthus roseus) Explore W8JMV4 Go to UniProtKB: W8JMV4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8JMV4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL (Subject of Investigation/LOI) Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.221 (Depositor), 0.221 (DCC)
R-Value Work: 0.187 (Depositor), 0.186 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.741	α = 90
b = 52.667	β = 90
c = 202.111	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-24

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-01-24
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.