9L6J | pdb_00009l6j

Structural studies on the conformation changes induced by ligand binding in an Adenine phosphoribosyltransferase (FnAPRT) from Fusobacterium nucleatum

PDB DOI: https://doi.org/10.2210/pdb9L6J/pdb

Classification: TRANSFERASE
Organism(s): Fusobacterium nucleatum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-24 Released: 2025-12-24
Deposition Author(s): Kim, B., Hwang, J., Do, H., Lee, J.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free:
0.226 (Depositor), 0.235 (DCC)
R-Value Work:
0.221 (Depositor), 0.222 (DCC)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural studies on the conformation changes induced by ligand binding in an Adenine phosphoribosyltransferase (FnAPRT) from Fusobacterium nucleatum

Kim, B., Hwang, J., Do, H., Lee, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 19.38 kDa
Atom Count: 1,396
Modeled Residue Count: 170
Deposited Residue Count: 170
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine phosphoribosyltransferase	A [auth B]	170	Fusobacterium nucleatum	Mutation(s): 0 Gene Names: apt, FN1483 EC: 2.4.2.7
UniProt
Find proteins for Q8RDM9 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RDM9 Go to UniProtKB: Q8RDM9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RDM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.226 (Depositor), 0.235 (DCC)
R-Value Work: 0.221 (Depositor), 0.222 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.048	α = 90
b = 106.523	β = 90
c = 47.807	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2025-12-24
Type: Initial release

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.