9HEN | pdb_00009hen

Crystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, double mutation V90P and V136M(NuoE), bound to NAD+

PDB DOI: https://doi.org/10.2210/pdb9HEN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aquifex aeolicus VF5
Expression System: Escherichia coli B
Mutation(s): Yes

Deposited: 2024-11-14 Released: 2025-11-05
Deposition Author(s): Wohlwend, D., Friedrich, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.182 (Depositor), 0.187 (DCC)
R-Value Work:
0.162 (Depositor), 0.170 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I

Wohlwend, D., Gnandt, E., Vranas, M., Gerhardt, S., Friedrich, T.

To be published.

Macromolecule Content

Total Structure Weight: 137.83 kDa
Atom Count: 10,119
Modeled Residue Count: 1,152
Deposited Residue Count: 1,188
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit E	A, C	160	Aquifex aeolicus VF5	Mutation(s): 2 Gene Names: nuoE, aq_574 EC: 7.1.1
UniProt
Find proteins for O66842 (Aquifex aeolicus (strain VF5)) Explore O66842 Go to UniProtKB: O66842
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O66842
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit F	B, D	434	Aquifex aeolicus VF5	Mutation(s): 0 Gene Names: nuoF EC: 7.1.1
UniProt
Find proteins for O66841 (Aquifex aeolicus (strain VF5)) Explore O66841 Go to UniProtKB: O66841
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O66841
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain H [auth B] MOL2 format, chain M [auth D] MOL2 format, chain H [auth B] mmCIF format, chain M [auth D] mmCIF format, chain H [auth B]	H [auth B], M [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain H [auth B] Focus chain M [auth D] Interactions & Density Focus chain H [auth B] Focus chain M [auth D]
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain L [auth D] MOL2 format, chain G [auth B] MOL2 format, chain L [auth D] mmCIF format, chain G [auth B] mmCIF format, chain L [auth D]	G [auth B], L [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain G [auth B] Focus chain L [auth D] Interactions & Density Focus chain G [auth B] Focus chain L [auth D]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain F [auth B] MOL2 format, chain K [auth D] MOL2 format, chain F [auth B] mmCIF format, chain K [auth D] mmCIF format, chain F [auth B]	F [auth B], K [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain K [auth D] Interactions & Density Focus chain F [auth B] Focus chain K [auth D]
FES (Subject of Investigation/LOI) Query on FES Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain E [auth A]	E [auth A], J [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth C]
BU3 Query on BU3 Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D]	N [auth D], O [auth D]	(R,R)-2,3-BUTANEDIOL C₄ H₁₀ O₂ OWBTYPJTUOEWEK-QWWZWVQMSA-N		Interactions Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain N [auth D] Focus chain O [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain I [auth B] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain I [auth B] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain I [auth B]	I [auth B], Q [auth D], R [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain I [auth B] Focus chain Q [auth D] Focus chain R [auth D]