9FPK | pdb_00009fpk

Ni,Fe-CODH : Eu(II)-reduced pH 8.0

PDB DOI: https://doi.org/10.2210/pdb9FPK/pdb

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

Deposited: 2024-06-13 Released: 2025-07-30
Deposition Author(s): Basak, Y., Jeoung, J.-H., Dobbek, H.
Funding Organization(s): German Research Foundation (DFG), Germanys Excellence Strategy

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free:
0.169 (Depositor), 0.168 (DCC)
R-Value Work:
0.142 (Depositor), 0.143 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Ni,Fe-CODH : Ti(III)-reduced pH 8.0

Basak, Y., Jeoung, J.-H., Dobbek, H.

(2025) Nature Catalysis

DOI: https://doi.org/10.1038/s41929-025-01388-5

Macromolecule Content

Total Structure Weight: 68.36 kDa
Atom Count: 5,884
Modeled Residue Count: 634
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase 2	A [auth X]	636	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0 Gene Names: cooS2, cooSII, CHY_0085 EC: 1.2.7.4
UniProt
Find proteins for Q9F8A8 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q9F8A8 Go to UniProtKB: Q9F8A8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9F8A8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 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 X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
F3S (Subject of Investigation/LOI) Query on F3S Download Ideal Coordinates CCD File SDF format, chain D [auth X] MOL2 format, chain D [auth X] mmCIF format, chain D [auth X]	D [auth X]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain D [auth X] Interactions & Density Focus chain D [auth X]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain I [auth X] MOL2 format, chain I [auth X] mmCIF format, chain I [auth X]	I [auth X]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth X] Interactions & Density Focus chain I [auth X]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth X] SDF format, chain K [auth X] MOL2 format, chain J [auth X] MOL2 format, chain K [auth X] mmCIF format, chain J [auth X] mmCIF format, chain K [auth X]	J [auth X], K [auth X]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth X] Focus chain K [auth X] Interactions & Density Focus chain J [auth X] Focus chain K [auth X]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain F [auth X] MOL2 format, chain F [auth X] mmCIF format, chain F [auth X]	F [auth X]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth X] Interactions & Density Focus chain F [auth X]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain E [auth X] MOL2 format, chain E [auth X] mmCIF format, chain E [auth X]	E [auth X]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth X] Interactions & Density Focus chain E [auth X]
CO2 (Subject of Investigation/LOI) Query on CO2 Download Ideal Coordinates CCD File SDF format, chain H [auth X] MOL2 format, chain H [auth X] mmCIF format, chain H [auth X]	H [auth X]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Interactions Focus chain H [auth X] Interactions & Density Focus chain H [auth X]
CMO (Subject of Investigation/LOI) Query on CMO Download Ideal Coordinates CCD File SDF format, chain G [auth X] MOL2 format, chain G [auth X] mmCIF format, chain G [auth X]	G [auth X]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain G [auth X] Interactions & Density Focus chain G [auth X]