8RPL

AMP-forming acetyl-CoA synthetase from Chloroflexota bacterium with bound acetyl AMP

PDB DOI: https://doi.org/10.2210/pdb8RPL/pdb

Classification: LIGASE
Organism(s): Chloroflexota bacterium
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-01-16 Released: 2024-06-19
Deposition Author(s): Striska, K., Palm, G.J., Lammers, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.201
R-Value Work: 0.161

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The AMP-forming acetyl-CoA-synthetase is regulated by lysine acetylation and has an intrinsic phosphotransacetylase activity to adjust its activity to the cellular acetyl-phosphate level

Qin, C., Lammers, M.

(2024) Nature Comm

Macromolecule Content

Total Structure Weight: 299.07 kDa
Atom Count: 20,543
Modelled Residue Count: 2,510
Deposited Residue Count: 2,628
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetate--CoA ligase	A, B, C, D	657	Chloroflexota bacterium	Mutation(s): 0 Gene Names: acs, E6J36_13485 EC: 6.2.1.1
UniProt
Find proteins for A0A535FEC2 (Chloroflexota bacterium) Explore A0A535FEC2 Go to UniProtKB: A0A535FEC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A535FEC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6R9 (Subject of Investigation/LOI) Query on 6R9 Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B], K [auth C], N [auth D]	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate C₁₂ H₁₆ N₅ O₈ P UBPVOHPZRZIJHM-WOUKDFQISA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth D] SDF format, chain F [auth A] SDF format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C]	F [auth A], I [auth B], L [auth C], O [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A]	G [auth A], J [auth B], M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D]	P [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]