9LQF | pdb_00009lqf

Crystal structure of SAM lyase in complex with SAH-AMP

PDB DOI: https://doi.org/10.2210/pdb9LQF/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: 1.59 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.186 (Depositor), 0.186 (DCC)
R-Value Observed:
0.188 (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: 181.21 kDa
Atom Count: 13,896
Modeled Residue Count: 1,478
Deposited Residue Count: 1,500
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM lyase	A B [auth D] C [auth E] D [auth B] E [auth C] A, B [auth D], C [auth E], D [auth B], E [auth C], F, G, H, I, J, K, L	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5I3U9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 BA [auth I] SDF format, chain CA [auth J] SDF format, chain EA [auth K] SDF format, chain GA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth D] SDF format, chain P [auth E] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain W [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain BA [auth I] MOL2 format, chain CA [auth J] MOL2 format, chain EA [auth K] MOL2 format, chain GA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain BA [auth I] mmCIF format, chain CA [auth J] mmCIF format, chain EA [auth K] mmCIF format, chain GA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	BA [auth I] CA [auth J] EA [auth K] GA [auth L] M [auth A] BA [auth I], CA [auth J], EA [auth K], GA [auth L], M [auth A], O [auth D], P [auth E], R [auth B], T [auth C], W [auth F], X [auth G], Z [auth H]	(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 BA [auth I] Focus chain CA [auth J] Focus chain EA [auth K] Focus chain GA [auth L] Focus chain M [auth A] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth B] Focus chain T [auth C] Focus chain W [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain CA [auth J] Focus chain EA [auth K] Focus chain GA [auth L] Focus chain M [auth A] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth B] Focus chain T [auth C] Focus chain W [auth F] Focus chain X [auth G] Focus chain Z [auth H]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain DA [auth J] SDF format, chain FA [auth K] SDF format, chain N [auth A] SDF format, chain Q [auth E] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain V [auth F] SDF format, chain Y [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain DA [auth J] MOL2 format, chain FA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain AA [auth H] mmCIF format, chain DA [auth J] mmCIF format, chain FA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth F] mmCIF format, chain Y [auth G]	AA [auth H] DA [auth J] FA [auth K] N [auth A] Q [auth E] AA [auth H], DA [auth J], FA [auth K], N [auth A], Q [auth E], S [auth B], U [auth C], V [auth F], Y [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain N [auth A] Focus chain Q [auth E] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain N [auth A] Focus chain Q [auth E] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth F] Focus chain Y [auth G]