7ZKJ | pdb_00007zkj

CODH/ACS complex of C. hydrogenoformans

PDB DOI: https://doi.org/10.2210/pdb7ZKJ/pdb

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

Deposited: 2022-04-13 Released: 2022-11-02
Deposition Author(s): Ruickoldt, J., Jeoung, J.-H., Basak, Y., Domnik, L., Dobbek, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.199 (Depositor)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.175 (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

On the Kinetics of CO2 Reduction by Ni, Fe-CO Dehydrogenases

Ruickoldt, J., Basak, Y., Domnik, L., Jeoung, J.H., Dobbek, H.

(2022) Acs Catal

DOI: https://doi.org/10.1021/acscatal.2c02221

Macromolecule Content

Total Structure Weight: 157.4 kDa
Atom Count: 11,930
Modeled Residue Count: 1,399
Deposited Residue Count: 1,399
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase	A	669	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0 Gene Names: ciss_06270 EC: 1.2.7.4
UniProt
Find proteins for A0A1L8D0M5 (Carboxydothermus islandicus) Explore A0A1L8D0M5 Go to UniProtKB: A0A1L8D0M5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1L8D0M5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CO-methylating acetyl-CoA synthase	B	730	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3ACS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RQM (Subject of Investigation/LOI) Query on RQM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	Fe(3)-Ni(1)-S(4) cluster Fe₄ Ni S₄ QGLWBXDZIHZONR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	D [auth A], E [auth A], K [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B]	M [auth B], N [auth B], O [auth B], P [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
NI (Subject of Investigation/LOI) Query on NI Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B]	J [auth B], L [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth B] Interactions & Density Focus chain J [auth B] Focus chain L [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
OH Query on OH 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]	HYDROXIDE ION H O XLYOFNOQVPJJNP-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]