9J9C

Glucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin and UDP2Fglucose in the presence of retinol

PDB DOI: https://doi.org/10.2210/pdb9J9C/pdb
Entry: 9J9C supersedes: 8J2S

Classification: TRANSFERASE
Organism(s): Nicotiana benthamiana
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-08-22 Released: 2024-09-04
Deposition Author(s): Arold, S.T., Hameed, U.F.S.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.318
R-Value Work: 0.256
R-Value Observed: 0.259

Starting Model: experimental
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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

Glucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin and UDP2Fglucose in the presence of retinol

Arold, S.T., Hameed, U.F.S.

To be published.

Macromolecule Content

Total Structure Weight: 377.35 kDa
Atom Count: 25,789
Modelled Residue Count: 3,218
Deposited Residue Count: 3,318
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, B, C, D, E A, B, C, D, E, F, G	474	Nicotiana benthamiana	Mutation(s): 0 EC: 2.4.1
UniProt
Find proteins for A0A8K1ZRH3 (Nicotiana benthamiana) Explore A0A8K1ZRH3 Go to UniProtKB: A0A8K1ZRH3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8K1ZRH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U2F Query on U2F Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain S [auth G] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain S [auth G] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain S [auth G]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], Q [auth F], S [auth G]	URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE C₁₅ H₂₃ F N₂ O₁₆ P₂ NGTCPFGWXMBZEP-NQQHDEILSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain S [auth G] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain S [auth G]
T83 (Subject of Investigation/LOI) Query on T83 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain R [auth F] SDF format, chain O [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth F] MOL2 format, chain O [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth F] mmCIF format, chain O [auth D]	I [auth A], K [auth B], M [auth C], O [auth D], R [auth F]	7-hydroxy-6-methoxy-2H-1-benzopyran-2-one C₁₀ H₈ O₄ RODXRVNMMDRFIK-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth F] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth F]