9LQC | pdb_00009lqc

Crystal structure of NrN D119A in complex with SAH-AMP

PDB DOI: https://doi.org/10.2210/pdb9LQC/pdb

Classification: IMMUNE SYSTEM
Organism(s): Bacteroides fragilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-01-28 Released: 2025-11-26
Deposition Author(s): Duan, B., Zhao, B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.293 (Depositor), 0.291 (DCC)
R-Value Work:
0.255 (Depositor), 0.256 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Mechanisms of SAM-AMP synthesis and degradation in antiviral type III CRISPR signaling.

Duan, B., Zhao, B.

To be published.

Macromolecule Content

Total Structure Weight: 122.68 kDa
Atom Count: 8,803
Modeled Residue Count: 1,004
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NrN	A, B, C, D	260	Bacteroides fragilis	Mutation(s): 1 Gene Names: CQW34_02202, F2Z29_06630, F2Z89_11900, F3B44_04915, FSA03_20595, NXX45_16660
UniProt
Find proteins for A0A2M9V7I2 (Bacteroides fragilis) Explore A0A2M9V7I2 Go to UniProtKB: A0A2M9V7I2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2M9V7I2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EL0 (Subject of Investigation/LOI) Query on A1EL0 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	(2~{S})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methylsulfanyl]-2-azanyl-butanoic acid C₂₄ H₃₂ N₁₁ O₁₁ P S QBCXMARFZQJLMA-XPJWLEQASA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.293 (Depositor), 0.291 (DCC)
R-Value Work: 0.255 (Depositor), 0.256 (DCC)
R-Value Observed: 0.257 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.668	α = 90
b = 121.609	β = 90.31
c = 72.579	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-26

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: 2025-11-26
Type: Initial release

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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.