9LED | pdb_00009led

Rice FBA1 in complex with fructose bisphosphate

PDB DOI: https://doi.org/10.2210/pdb9LED/pdb

Classification: HYDROLASE
Organism(s): Oryza sativa Japonica Group
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-07 Released: 2026-01-14
Deposition Author(s): Gao, A.M., Zhou, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.207 (Depositor), 0.207 (DCC)
R-Value Work:
0.190 (Depositor), 0.191 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Rice FBA1 in complex with fructose bisphosphate

Gao, A.M., Zhou, C.

To be published.

Macromolecule Content

Total Structure Weight: 74.6 kDa
Atom Count: 5,469
Modeled Residue Count: 677
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-bisphosphate aldolase 1, cytoplasmic	A, B	340	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: FBA1, FBA, Os05g0402700, LOC_Os05g33380, OSJNBa0035J16.18, OSJNBb0006J12.6 EC: 4.1.2.13
UniProt
Find proteins for P17784 (Oryza sativa subsp. japonica) Explore P17784 Go to UniProtKB: P17784
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17784
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6F (Subject of Investigation/LOI) Query on P6F Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	1,6-di-O-phosphono-D-fructose C₆ H₁₄ O₁₂ P₂ XPYBSIWDXQFNMH-UYFOZJQFSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.207 (Depositor), 0.207 (DCC)
R-Value Work: 0.190 (Depositor), 0.191 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.137	α = 90
b = 102.384	β = 93.11
c = 92.98	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-14

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-01-14
Type: Initial release

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