7Q5Y | pdb_00007q5y

Structure of NADH:ubichinon oxidoreductase (complex I) of the hyperthermophilic eubacterium Aquifex aeolicus

PDB DOI: https://doi.org/10.2210/pdb7Q5Y/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aquifex aeolicus VF5
Mutation(s): No

Deposited: 2021-11-05 Released: 2022-11-16
Deposition Author(s): Warkentin, E., Ermler, U., Peng, G.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.209 (Depositor), 0.208 (DCC)
R-Value Work:
0.169 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of NADH:ubichinon oxidoreductase (complex I) of the hyperthermophilic eubacterium Aquifex aeolicus

Warkentin, E., Ermler, U., Peng, G.

To be published.

Macromolecule Content

Total Structure Weight: 1,015.91 kDa
Atom Count: 69,025
Modeled Residue Count: 8,468
Deposited Residue Count: 8,736
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase I chain G	A, G, M, S	632	Aquifex aeolicus VF5	Mutation(s): 0
UniProt
Find proteins for O66748 (Aquifex aeolicus (strain VF5)) Explore O66748 Go to UniProtKB: O66748
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O66748
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit C/D 2	B, H, N, T	586	Aquifex aeolicus VF5	Mutation(s): 0 EC: 7.1.1
UniProt
Find proteins for O67335 (Aquifex aeolicus (strain VF5)) Explore O67335 Go to UniProtKB: O67335
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O67335
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit F	C, I, O, U	426	Aquifex aeolicus VF5	Mutation(s): 0 EC: 7.1.1
UniProt
Find proteins for O66841 (Aquifex aeolicus (strain VF5)) Explore O66841 Go to UniProtKB: O66841
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O66841
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit I	D, J, P, V	201	Aquifex aeolicus VF5	Mutation(s): 0 EC: 7.1.1
UniProt
Find proteins for O67337 (Aquifex aeolicus (strain VF5)) Explore O67337 Go to UniProtKB: O67337
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O67337
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit E	E, K, Q, W	160	Aquifex aeolicus VF5	Mutation(s): 0 EC: 7.1.1
UniProt
Find proteins for O66842 (Aquifex aeolicus (strain VF5)) Explore O66842 Go to UniProtKB: O66842
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O66842
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit B	F, L, R, X	179	Aquifex aeolicus VF5	Mutation(s): 0 EC: 7.1.1
UniProt
Find proteins for O67334 (Aquifex aeolicus (strain VF5)) Explore O67334 Go to UniProtKB: O67334
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O67334
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain ZA [auth O] SDF format, chain OA [auth I] SDF format, chain KB [auth U] SDF format, chain DA [auth C] MOL2 format, chain ZA [auth O] MOL2 format, chain OA [auth I] MOL2 format, chain KB [auth U] MOL2 format, chain DA [auth C] mmCIF format, chain ZA [auth O] mmCIF format, chain OA [auth I] mmCIF format, chain KB [auth U] mmCIF format, chain DA [auth C]	DA [auth C], KB [auth U], OA [auth I], ZA [auth O]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain DA [auth C] Focus chain KB [auth U] Focus chain OA [auth I] Focus chain ZA [auth O] Interactions & Density Focus chain DA [auth C] Focus chain KB [auth U] Focus chain OA [auth I] Focus chain ZA [auth O]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain JA [auth G] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain XA [auth M] SDF format, chain WA [auth M] SDF format, chain VA [auth M] SDF format, chain UA [auth M] SDF format, chain TA [auth L] SDF format, chain RA [auth J] SDF format, chain QA [auth J] SDF format, chain PB [auth X] SDF format, chain PA [auth I] SDF format, chain NB [auth V] SDF format, chain MB [auth V] SDF format, chain MA [auth G] SDF format, chain LB [auth U] SDF format, chain LA [auth G] SDF format, chain KA [auth G] SDF format, chain IB [auth S] SDF format, chain IA [auth F] SDF format, chain HB [auth S] SDF format, chain GB [auth S] SDF format, chain GA [auth D] SDF format, chain FB [auth S] SDF format, chain FA [auth D] SDF format, chain EB [auth R] SDF format, chain EA [auth C] SDF format, chain CB [auth P] SDF format, chain BB [auth P] SDF format, chain BA [auth A] SDF format, chain AB [auth O] SDF format, chain AA [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth M] MOL2 format, chain WA [auth M] MOL2 format, chain VA [auth M] MOL2 format, chain UA [auth M] MOL2 format, chain TA [auth L] MOL2 format, chain RA [auth J] MOL2 format, chain QA [auth J] MOL2 format, chain PB [auth X] MOL2 format, chain PA [auth I] MOL2 format, chain NB [auth V] MOL2 format, chain MB [auth V] MOL2 format, chain MA [auth G] MOL2 format, chain LB [auth U] MOL2 format, chain LA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain IB [auth S] MOL2 format, chain IA [auth F] MOL2 format, chain HB [auth S] MOL2 format, chain GB [auth S] MOL2 format, chain GA [auth D] MOL2 format, chain FB [auth S] MOL2 format, chain FA [auth D] MOL2 format, chain EB [auth R] MOL2 format, chain EA [auth C] MOL2 format, chain CB [auth P] MOL2 format, chain BB [auth P] MOL2 format, chain BA [auth A] MOL2 format, chain AB [auth O] MOL2 format, chain AA [auth A] mmCIF format, chain JA [auth G] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth M] mmCIF format, chain WA [auth M] mmCIF format, chain VA [auth M] mmCIF format, chain UA [auth M] mmCIF format, chain TA [auth L] mmCIF format, chain RA [auth J] mmCIF format, chain QA [auth J] mmCIF format, chain PB [auth X] mmCIF format, chain PA [auth I] mmCIF format, chain NB [auth V] mmCIF format, chain MB [auth V] mmCIF format, chain MA [auth G] mmCIF format, chain LB [auth U] mmCIF format, chain LA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain IB [auth S] mmCIF format, chain IA [auth F] mmCIF format, chain HB [auth S] mmCIF format, chain GB [auth S] mmCIF format, chain GA [auth D] mmCIF format, chain FB [auth S] mmCIF format, chain FA [auth D] mmCIF format, chain EB [auth R] mmCIF format, chain EA [auth C] mmCIF format, chain CB [auth P] mmCIF format, chain BB [auth P] mmCIF format, chain BA [auth A] mmCIF format, chain AB [auth O] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth O] BA [auth A] BB [auth P] CB [auth P] AA [auth A], AB [auth O], BA [auth A], BB [auth P], CB [auth P], EA [auth C], EB [auth R], FA [auth D], FB [auth S], GA [auth D], GB [auth S], HB [auth S], IA [auth F], IB [auth S], JA [auth G], KA [auth G], LA [auth G], LB [auth U], MA [auth G], MB [auth V], NB [auth V], PA [auth I], PB [auth X], QA [auth J], RA [auth J], TA [auth L], UA [auth M], VA [auth M], WA [auth M], XA [auth M], Y [auth A], Z [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth O] Focus chain BA [auth A] Focus chain BB [auth P] Focus chain CB [auth P] Focus chain EA [auth C] Focus chain EB [auth R] Focus chain FA [auth D] Focus chain FB [auth S] Focus chain GA [auth D] Focus chain GB [auth S] Focus chain HB [auth S] Focus chain IA [auth F] Focus chain IB [auth S] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain LB [auth U] Focus chain MA [auth G] Focus chain MB [auth V] Focus chain NB [auth V] Focus chain PA [auth I] Focus chain PB [auth X] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain TA [auth L] Focus chain UA [auth M] Focus chain VA [auth M] Focus chain WA [auth M] Focus chain XA [auth M] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth O] Focus chain BA [auth A] Focus chain BB [auth P] Focus chain CB [auth P] Focus chain EA [auth C] Focus chain EB [auth R] Focus chain FA [auth D] Focus chain FB [auth S] Focus chain GA [auth D] Focus chain GB [auth S] Focus chain HB [auth S] Focus chain IA [auth F] Focus chain IB [auth S] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain LB [auth U] Focus chain MA [auth G] Focus chain MB [auth V] Focus chain NB [auth V] Focus chain PA [auth I] Focus chain PB [auth X] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain TA [auth L] Focus chain UA [auth M] Focus chain VA [auth M] Focus chain WA [auth M] Focus chain XA [auth M] Focus chain Y [auth A] Focus chain Z [auth A]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain YA [auth M] SDF format, chain SA [auth K] SDF format, chain OB [auth W] SDF format, chain NA [auth G] SDF format, chain JB [auth S] SDF format, chain HA [auth E] SDF format, chain DB [auth Q] SDF format, chain CA [auth A] MOL2 format, chain YA [auth M] MOL2 format, chain SA [auth K] MOL2 format, chain OB [auth W] MOL2 format, chain NA [auth G] MOL2 format, chain JB [auth S] MOL2 format, chain HA [auth E] MOL2 format, chain DB [auth Q] MOL2 format, chain CA [auth A] mmCIF format, chain YA [auth M] mmCIF format, chain SA [auth K] mmCIF format, chain OB [auth W] mmCIF format, chain NA [auth G] mmCIF format, chain JB [auth S] mmCIF format, chain HA [auth E] mmCIF format, chain DB [auth Q] mmCIF format, chain CA [auth A]	CA [auth A] DB [auth Q] HA [auth E] JB [auth S] NA [auth G] CA [auth A], DB [auth Q], HA [auth E], JB [auth S], NA [auth G], OB [auth W], SA [auth K], YA [auth M]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain DB [auth Q] Focus chain HA [auth E] Focus chain JB [auth S] Focus chain NA [auth G] Focus chain OB [auth W] Focus chain SA [auth K] Focus chain YA [auth M] Interactions & Density Focus chain CA [auth A] Focus chain DB [auth Q] Focus chain HA [auth E] Focus chain JB [auth S] Focus chain NA [auth G] Focus chain OB [auth W] Focus chain SA [auth K] Focus chain YA [auth M]