8ZI7 | pdb_00008zi7

Crystal structure of SrUGT76G4 in complex with Rubusoside

PDB DOI: https://doi.org/10.2210/pdb8ZI7/pdb

Classification: TRANSFERASE
Organism(s): Stevia rebaudiana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-13 Released: 2025-05-21
Deposition Author(s): Wang, Y., Li, T., Yin, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.232 (Depositor), 0.235 (DCC)
R-Value Work:
0.183 (Depositor), 0.192 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Functional Characterization and Structural Insights into SrUGT76G1-4 from Stevia Rebaudioside Reveal a Residue Critical for the Regioselectivity and efficient Rebaudioside M synthesis

Wang, Y., Li, T., Yin, H.

To be published.

Macromolecule Content

Total Structure Weight: 53.16 kDa
Atom Count: 3,412
Modeled Residue Count: 403
Deposited Residue Count: 458
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UGT-glycosyltransferase 76G4	A	458	Stevia rebaudiana	Mutation(s): 0 EC: 2.4.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AQ9 (Subject of Investigation/LOI) Query on AQ9 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-O-[(8alpha,9beta,10alpha,13alpha)-13-(beta-D-glucopyranosyloxy)-18-oxokaur-16-en-18-yl]-beta-D-glucopyranose C₃₂ H₅₀ O₁₃ YWPVROCHNBYFTP-OSHKXICASA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A]	D [auth A], H [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain H [auth A]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A]	E [auth A], I [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain I [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]