8PU1 | pdb_00008pu1

Structure of the toxin/antitoxin complex FaRel/ATfaRel2 with APCPP

PDB DOI: https://doi.org/10.2210/pdb8PU1/pdb

Classification: ANTITOXIN
Organism(s): Thomasclavelia ramosa
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-07-16 Released: 2024-07-24
Deposition Author(s): Garcia-Pino, A., Talavera Perez, A., Dominguez Molina, L.
Funding Organization(s): Fonds National de la Recherche Scientifique (FNRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.246 (Depositor), 0.230 (DCC)
R-Value Work:
0.224 (Depositor), 0.220 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of the toxin/antitoxin complex FaRel/ATfaRel2 with APCPP

Garcia-Pino, A., Talavera Perez, A., Dominguez Molina, L.

To be published.

Macromolecule Content

Total Structure Weight: 34.85 kDa
Atom Count: 2,572
Modeled Residue Count: 266
Deposited Residue Count: 282
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATfaRel2	A	75	Thomasclavelia ramosa	Mutation(s): 0 Gene Names: DXB93_19740
UniProt
Find proteins for A0A3E3DY87 (Thomasclavelia ramosa) Explore A0A3E3DY87 Go to UniProtKB: A0A3E3DY87
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3E3DY87
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RelA/SpoT domain-containing protein	B	207	Thomasclavelia ramosa	Mutation(s): 1 Gene Names: DXB93_19735
UniProt
Find proteins for A0A3E3DY42 (Thomasclavelia ramosa) Explore A0A3E3DY42 Go to UniProtKB: A0A3E3DY42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3E3DY42
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APC (Subject of Investigation/LOI) Query on APC Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ CAWZRIXWFRFUQB-IOSLPCCCSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	F [auth A], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain Q [auth B] Focus chain R [auth B]
POL Query on POL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	C [auth A] E [auth A] G [auth A] I [auth A] J [auth A] C [auth A], E [auth A], G [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B]	N-PROPANOL C₃ H₈ O BDERNNFJNOPAEC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	H [auth A], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B]