9XUL | pdb_00009xul

Pi-bound ADP-Glucose Pyrophosphorylase

PDB DOI: https://doi.org/10.2210/pdb9XUL/pdb
EM Map EMD-67270: EMDB EMDataResource

Classification: PLANT PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-11-24 Released: 2026-04-08
Deposition Author(s): Wu, Y.T., Lin, H.J., Fan, M.R.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9XUL

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

Literature

Pi-bound ADP-Glucose Pyrophosphorylase

Wu, Y.T., Lin, H.J., Fan, M.R.

To be published.

Macromolecule Content

Total Structure Weight: 208.67 kDa
Atom Count: 13,424
Modeled Residue Count: 1,720
Deposited Residue Count: 1,894
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic	A, C	470	Arabidopsis thaliana	Mutation(s): 0 Gene Names: APS1, ADG1, APS, At5g48300, K23F3.2 EC: 2.7.7.27
UniProt
Find proteins for P55228 (Arabidopsis thaliana) Explore P55228 Go to UniProtKB: P55228
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55228
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic	B, D	477	Arabidopsis thaliana	Mutation(s): 0 Gene Names: ADG2, APL1, At5g19220, T24G5.120 EC: 2.7.7.27
UniProt
Find proteins for P55229 (Arabidopsis thaliana) Explore P55229 Go to UniProtKB: P55229
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55229
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth D] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D]	E [auth A] F [auth B] G [auth B] H [auth C] I [auth D] E [auth A], F [auth B], G [auth B], H [auth C], I [auth D], J [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB0630101

Revision History (Full details and data files)

Version 1.0: 2026-04-08
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.