7O0D | pdb_00007o0d

monomeric acetyl-CoA synthase in open conformation with methanethiol moiety of CoA bound to nickel proximal

PDB DOI: https://doi.org/10.2210/pdb7O0D/pdb

Classification: OXIDOREDUCTASE
Organism(s): Carboxydothermus hydrogenoformans Z-2901
Expression System: Escherichia coli M15
Mutation(s): No

Deposited: 2021-03-26 Released: 2022-04-13
Deposition Author(s): Kreibich, J., Jeoung, J.H., Dobbek, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.222 (Depositor), 0.230 (DCC)
R-Value Work:
0.196 (Depositor), 0.210 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Ligand binding at the Ni,Ni-[4Fe-4S] cluster of acetyl-CoA synthase

Kreibich, J., Jeoung, J.H., Dobbek, H.

To be published.

Macromolecule Content

Total Structure Weight: 86.04 kDa
Atom Count: 6,261
Modeled Residue Count: 729
Deposited Residue Count: 734
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CO-methylating acetyl-CoA synthase	A	734	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0 Gene Names: acsB, CHY_1222 EC: 2.3.1.169
UniProt
Find proteins for Q3ACS4 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q3ACS4 Go to UniProtKB: Q3ACS4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3ACS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PG6 Query on PG6 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain X [auth A] SDF format, chain T [auth A] SDF format, chain F [auth A] MOL2 format, chain J [auth A] MOL2 format, chain X [auth A] MOL2 format, chain T [auth A] MOL2 format, chain F [auth A] mmCIF format, chain J [auth A] mmCIF format, chain X [auth A] mmCIF format, chain T [auth A] mmCIF format, chain F [auth A]	F [auth A], J [auth A], T [auth A], X [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain T [auth A] Focus chain X [auth A] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain T [auth A] Focus chain X [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain V [auth A] SDF format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain V [auth A] MOL2 format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain V [auth A] mmCIF format, chain S [auth A]	R [auth A], S [auth A], V [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth A] Interactions & Density Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A]	G [auth A], K [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth A] Interactions & Density Focus chain G [auth A] Focus chain K [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain U [auth A] SDF format, chain W [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain U [auth A] mmCIF format, chain W [auth A]	H [auth A], I [auth A], U [auth A], W [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain U [auth A] Focus chain W [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain U [auth A] Focus chain W [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	L [auth A] M [auth A] N [auth A] O [auth A] P [auth A] L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
MEE (Subject of Investigation/LOI) Query on MEE Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	METHANETHIOL C H₄ S LSDPWZHWYPCBBB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]