9JN3 | pdb_00009jn3

Crystal structure of AvpGT in complex with Ara-A

PDB DOI: https://doi.org/10.2210/pdb9JN3/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces sp. AVP053U2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-22 Released: 2025-01-29
Deposition Author(s): Li, J.H., Wang, Z.Q., Zhang, Z.Y., Chen, W.Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.248 (Depositor), 0.247 (DCC)
R-Value Work:
0.181 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

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

Efficient Synthesis of Glycodiversified Nucleoside Analogues by a Thermophilic Promiscuous Glycosyltransferase

Wang, Z., Li, J., Wang, X., Jin, B., Zhou, L., Zhao, Z., Gu, M., Song, X., Wang, J., Deng, Z., Wu, S., Zhang, Z., Chen, W.

(2025) ACS Catal 15: 1217-1229

DOI: https://doi.org/10.1021/acscatal.4c06506

Macromolecule Content

Total Structure Weight: 69.77 kDa
Atom Count: 4,824
Modeled Residue Count: 594
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GalNAc(5)-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase	A, B	306	Streptomyces sp. AVP053U2	Mutation(s): 0 Gene Names: pglI, APS67_002972 EC: 2.4.1.293
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
RAB (Subject of Investigation/LOI) Query on RAB Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	2-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-UHTZMRCNSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]