9UCE | pdb_00009uce

Crystal structure of glycosyltransferase UGT73K1 in complex with UDP

PDB DOI: https://doi.org/10.2210/pdb9UCE/pdb

Classification: TRANSFERASE
Organism(s): Medicago truncatula
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-04 Released: 2025-04-23
Deposition Author(s): Zhu, J.S., Zhang, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.208 (Depositor), 0.208 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (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

Crystal structure of glycosyltransferase UGT73K1 in complex with UDP

Zhu, J.S., Zhang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 58.44 kDa
Atom Count: 3,745
Modeled Residue Count: 453
Deposited Residue Count: 518
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	518	Medicago truncatula	Mutation(s): 0 Gene Names: 11431381, MTR_4g031800, MtrunA17_Chr4g0014061 EC: 2.4.1
UniProt
Find proteins for Q5IFH8 (Medicago truncatula) Explore Q5IFH8 Go to UniProtKB: Q5IFH8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5IFH8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A]	C [auth A], D [auth A], E [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	B [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain F [auth A] Focus chain G [auth A]