8ZNM | pdb_00008znm

CRYSTAL STRUCTURE OF DI-C-GLYCOSYLTRANSFERASE GGCGT MUTANT IN COMPLEX WITH UDP-GLC

PDB DOI: https://doi.org/10.2210/pdb8ZNM/pdb

Classification: TRANSFERASE
Organism(s): Glycyrrhiza glabra
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-05-27 Released: 2025-06-04
Deposition Author(s): Feng, X.D., Liu, X.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.217 (Depositor), 0.218 (DCC)
R-Value Work:
0.176 (Depositor), 0.177 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Computation-aided redesign of C-glycosyltransferases facilitates sustainable biosynthesis of C-glycosides

Liu, X., Li, J., Zhao, W., Gong, X., Sun, Q., Feng, X., Li, C.

(2026) Green Chem 28: 7961-7973

DOI: https://doi.org/10.1039/D6GC00247A

Macromolecule Content

Total Structure Weight: 210.7 kDa
Atom Count: 14,717
Modeled Residue Count: 1,799
Deposited Residue Count: 1,888
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GgCGT	A, B, C, D	472	Glycyrrhiza glabra	Mutation(s): 10
UniProt
Find proteins for A0A6I8WFN2 (Glycyrrhiza glabra) Explore A0A6I8WFN2 Go to UniProtKB: A0A6I8WFN2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6I8WFN2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG (Subject of Investigation/LOI) Query on UPG Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.217 (Depositor), 0.218 (DCC)
R-Value Work: 0.176 (Depositor), 0.177 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.618	α = 64.76
b = 81.849	β = 88.28
c = 94.141	γ = 88.24

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2018YFA0901800

Revision History (Full details and data files)

Version 1.0: 2025-06-04
Type: Initial release
Version 1.1: 2026-06-10
Changes: Database references

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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.