7NYS | pdb_00007nys

monomeric acetyl-CoA synthase in closed conformation with carbon monoxide bound to the Ni proximal of cluster A

PDB DOI: https://doi.org/10.2210/pdb7NYS/pdb

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

Deposited: 2021-03-23 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: 2.00 Å
R-Value Free:
0.221 (Depositor), 0.230 (DCC)
R-Value Work:
0.184 (Depositor), 0.200 (DCC)
R-Value Observed:
0.185 (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: 167.37 kDa
Atom Count: 13,255
Modeled Residue Count: 1,457
Deposited Residue Count: 1,466
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, B	733	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UW8 Query on UW8 Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	2-[3,8,8,12,12-pentakis(2-hydroxy-2-oxoethyl)-2,7,11-tris(oxidanylidene)-1,4,6,9,10,13-hexaoxa-5$l^{6}-titanaspiro[4.4^{5}.4^{5}]tridecan-3-yl]ethanoic acid C₁₈ H₁₈ O₂₁ Ti MTEIPJBPJJNUGP-UHFFFAOYSA-K		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain S [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain S [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	N [auth B], O [auth B], S [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth B]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B]	L [auth B], M [auth B], P [auth B], Q [auth B], R [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
UWE (Subject of Investigation/LOI) Query on UWE Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	$l^{3}-oxidanylidynemethylnickel C Ni O IBXNIJKRMDYAOR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]