9LQG | pdb_00009lqg

Crystal structure of SAM lyase in complex with MTA-AMP

PDB DOI: https://doi.org/10.2210/pdb9LQG/pdb

Classification: IMMUNE SYSTEM
Organism(s): Clostridium botulinum A str. Hall
Expression System: Escherichia coli
Mutation(s): No

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: 1.28 Å
R-Value Free:
0.209 (Depositor), 0.209 (DCC)
R-Value Work:
0.193 (Depositor), 0.194 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: in silico
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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

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: 45.11 kDa
Atom Count: 3,411
Modeled Residue Count: 370
Deposited Residue Count: 375
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM lyase	A, B, C	125	Clostridium botulinum A str. Hall	Mutation(s): 0 Gene Names: CBO2178
UniProt
Find proteins for A5I3U9 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore A5I3U9 Go to UniProtKB: A5I3U9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5I3U9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IJB (Subject of Investigation/LOI) Query on A1IJB Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B], I [auth C]	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl [(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-2-(methylsulfanylmethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate C₂₁ H₂₇ N₁₀ O₉ P S NNWVUANIXUHJMY-NAGRZYTCSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], H [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C]