3i9v

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 2 mol/ASU

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NADH-quinone oxidoreductase subunit 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 7 CALCIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 5 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQO1_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 1–438； UniProt 1–438 Author chain A； PDBConstruct 1–438； UniProt 1–438

NADH-quinone oxidoreductase subunit 2

OrganismNot specified

UniProt Q56221

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 7 CALCIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 5 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQO2_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 2； PDBConstruct 1–181； UniProt 1–181 Author chain B； PDBConstruct 1–181； UniProt 1–181

NADH-quinone oxidoreductase subunit 3

OrganismNot specified

UniProt Q56223

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 7 CALCIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 5 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQO3_THET8
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 3； PDBConstruct 1–783； UniProt 1–783 Author chain C； PDBConstruct 1–783； UniProt 1–783

NADH-quinone oxidoreductase subunit 4

OrganismNot specified

UniProt Q56220

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 7 CALCIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 5 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQO4_THET8
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain 4； PDBConstruct 1–409； UniProt 1–409 Author chain D； PDBConstruct 1–409； UniProt 1–409

NADH-quinone oxidoreductase subunit 5

OrganismNot specified

UniProt Q56219

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 7 CALCIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 5 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQO5_THET8
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain 5； PDBConstruct 1–207； UniProt 1–207 Author chain E； PDBConstruct 1–207； UniProt 1–207

NADH-quinone oxidoreductase subunit 6

OrganismNot specified

UniProt Q56218

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 7 CALCIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 5 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQO6_THET8
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain 6； PDBConstruct 1–181； UniProt 1–181 Author chain F； PDBConstruct 1–181； UniProt 1–181

NADH-quinone oxidoreductase subunit 9

OrganismNot specified

UniProt Q56224

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 7 CALCIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 15 × 1 （Q5SKZ7） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 5 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQO9_THET8
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain 9； PDBConstruct 1–182； UniProt 1–182 Author chain G； PDBConstruct 1–182； UniProt 1–182

NADH-quinone oxidoreductase subunit 15

OrganismNot specified

UniProt Q5SKZ7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 7 CALCIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	NADH-quinone oxidoreductase subunit 1 × 1 （Q56222） NADH-quinone oxidoreductase subunit 2 × 1 （Q56221） NADH-quinone oxidoreductase subunit 3 × 1 （Q56223） NADH-quinone oxidoreductase subunit 4 × 1 （Q56220） NADH-quinone oxidoreductase subunit 5 × 1 （Q56219） NADH-quinone oxidoreductase subunit 6 × 1 （Q56218） NADH-quinone oxidoreductase subunit 9 × 1 （Q56224） IRON/SULFUR CLUSTER × 7 FLAVIN MONONUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 2 MANGANESE (II) ION × 5 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQO15_THET8
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain 7； PDBConstruct 1–129； UniProt 1–129 Author chain H； PDBConstruct 1–129； UniProt 1–129

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3i9v
Deposition date deposition_date	2009-07-13
Structure title title	Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 2 mol/ASU
Keywords keywords	;OXIDOREDUCTASE, ELECTRON TRANSPORT, RESPIRATORY CHAIN, Cell membrane, Flavoprotein, FMN, Iron, Iron-sulfur, Membrane, Metal-binding, NAD, Quinone, Disulfide bond, Transport ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3i9v__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3i9v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3i9v__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	43.26 Å
Rg (electron density)	43.25 Å
Total Rg	43.19 Å
Atom count	18761
Residues	2368
Excluded volume	335660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3i9v__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3i9v__assembly_2__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Description description	NADH-quinone oxidoreductase subunit 1
Molecular weight formula_weight	48693.7 kDa
EC 编号 ec_number	1.6.99.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,A
Atom count atom_count	37520

MTGPILSGLDPRFERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRSGLRGRGGAGFPTGLKWSFMPKDDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMILAGYAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAYICGEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQMGTEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPLPFTEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCREGVAGFMVNLFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQYLALAREKRPVPRPSLWR

Entity 2 Entity 2 polymer

Description description	NADH-quinone oxidoreductase subunit 2
Molecular weight formula_weight	20309.2 kDa
EC 编号 ec_number	1.6.99.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2,B

MGFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEVMGVASFYSYYQFVPTGKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQKVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGKRLEEIELPGKCGHHVHEVEV

Entity 3 Entity 3 polymer

Description description	NADH-quinone oxidoreductase subunit 3
Molecular weight formula_weight	86656.2 kDa
EC 编号 ec_number	1.6.99.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3,C

MVRVKVNDRIVEVPPGTSVMDAVFHAGYDVPLFCSEKHLSPIGACRMCLVRIGLPKKGPDGKPLLNEKGEPEIQWQPKLAASCVTAVADGMVVDTLSDVVREAQAGMVEFTLLNHPLDCPTCDKGGACELQDRTVEYGLYEKYYQKGPLELPVYTRFEFTRRHVDKHHPLSPFVILDRERCIHCKRCVRYFEEVPGDEVLDFIERGVHTFIGTMDFGLPSGFSGNITDICPVGALLDLTARFRARNWEMEETPTTCALCPVGCGITADTRSGELLRIRAREVPEVNEIWICDAGRFGHEWADQNRLKTPLVRKEGRLVEATWEEAFLALKEGLKEARGEEVGLYLAHDATLEEGLLASELAKALKTPHLDFQGRTAAPASLFPPASLEDLLQADFALVLGDPTEEAPILHLRLSEFVRDLKPPHRYNHGTPFADLQIKERMPRRTDKMALFAPYRAPLMKWAAIHEVHRPGEEREILLALLGDKEGSEMVAKAKEAWEKAKNPVLILGAGVLQDTVAAERARLLAERKGAKVLAMTPAANARGLEAMGVLPGAKGASWDEPGALYAYYGFVPPEEALKGKRFVVMHLSHLHPLAERYAHVVLPAPTFYEKRGHLVNLEGRVLPLSPAPIENGEAEGALQVLALLAEALGVRPPFRLHLEAQKALKARKVPEAMGRLSFRLKELRPKERKGAFYLRPTMWKAHQAVGKAQEAARAELWAHPETARAEALPEGAQVAVETPFGRVEARVVHREDVPKGHLYLSALGPAAGLRVEGRVLVPAGGEA

Entity 4 Entity 4 polymer

Description description	NADH-quinone oxidoreductase subunit 4
Molecular weight formula_weight	46428.0 kDa
EC 编号 ec_number	1.6.99.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4,D

MREEFLEEIPLDAPPEEAKELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPGPVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR

Entity 5 Entity 5 polymer

Description description	NADH-quinone oxidoreductase subunit 5
Molecular weight formula_weight	23893.3 kDa
EC 编号 ec_number	1.6.99.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	5,E

MRLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAMGFNFLADIVGLDYLTYPDPRPERFAVVYELVSLPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYDLFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPGLTFYKGGSRKGYRSLWADLKKAREVKG

Entity 6 Entity 6 polymer

Description description	NADH-quinone oxidoreductase subunit 6
Molecular weight formula_weight	20262.6 kDa
EC 编号 ec_number	1.6.99.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	6,F

MALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFNNYAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGERLPPVAAWKRTRG

Entity 7 Entity 7 polymer

Description description	NADH-quinone oxidoreductase subunit 9
Molecular weight formula_weight	20106.3 kDa
EC 编号 ec_number	1.6.99.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	9,G

MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCAAACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFEMADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGGKR

Entity 8 Entity 8 polymer

Description description	NADH-quinone oxidoreductase subunit 15
Molecular weight formula_weight	14812.1 kDa
EC 编号 ec_number	1.6.99.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	7,H

MSASSERELYEAWVELLSWMREYAQAKGVRFEKEADFPDFIYRMERPYDLPTTIMTASLSDGLGEPFLLADVSPRHAKLKRIGLRLPRAHIHLHAHYEPGKGLVTGKIPLTKERFFALADRAREALAFA

Entity 9 Entity 9 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 10 Entity 10 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 12 Entity 12 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 13 Entity 13 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 46 domains

SCOP 2.08 (26 domains)

Domain ID domain_id	d3i9v11
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.142 — Nqo1 FMN-binding domain-like
Superfamily Superfamily superfamily	c.142.1 — Nqo1 FMN-binding domain-like
Family Family family	c.142.1.1 — Nqo1 FMN-binding domain-like

Domain ID domain_id	d3i9v12
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.13 — Nqo1 middle domain-like
Family Family family	d.15.13.0 — automated matches

Domain ID domain_id	d3i9v13
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.12 — Nqo1C-terminal domain-like
Family Family family	a.29.12.0 — automated matches

Domain ID domain_id	d3i9v2_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.21 — NQO2-like

Domain ID domain_id	d3i9v31
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.0 — automated matches

Domain ID domain_id	d3i9v32
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.0 — automated matches

Domain ID domain_id	d3i9v33
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

Domain ID domain_id	d3i9v34
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.0 — automated matches

Domain ID domain_id	d3i9v4_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.18 — HydB/Nqo4-like
Superfamily Superfamily superfamily	e.18.1 — HydB/Nqo4-like
Family Family family	e.18.1.2 — Nqo4-like

Domain ID domain_id	d3i9v5_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.307 — Nqo5-like
Superfamily Superfamily superfamily	d.307.1 — Nqo5-like
Family Family family	d.307.1.1 — Nqo5-like

Domain ID domain_id	d3i9v6_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.19 — HydA/Nqo6-like
Superfamily Superfamily superfamily	e.19.1 — HydA/Nqo6-like
Family Family family	e.19.1.2 — Nq06-like

Domain ID domain_id	d3i9v7_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.82 — N domain of copper amine oxidase-like
Superfamily Superfamily superfamily	d.82.2 — Frataxin/Nqo15-like
Family Family family	d.82.2.2 — Nqo15-like

Domain ID domain_id	d3i9v9_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

Domain ID domain_id	d3i9va1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.142 — Nqo1 FMN-binding domain-like
Superfamily Superfamily superfamily	c.142.1 — Nqo1 FMN-binding domain-like
Family Family family	c.142.1.1 — Nqo1 FMN-binding domain-like

Domain ID domain_id	d3i9va2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.13 — Nqo1 middle domain-like
Family Family family	d.15.13.0 — automated matches

Domain ID domain_id	d3i9va3
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.12 — Nqo1C-terminal domain-like
Family Family family	a.29.12.0 — automated matches

Domain ID domain_id	d3i9vb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.21 — NQO2-like

Domain ID domain_id	d3i9vc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.0 — automated matches

Domain ID domain_id	d3i9vc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.0 — automated matches

Domain ID domain_id	d3i9vc3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
Family Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

Domain ID domain_id	d3i9vc4
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.0 — automated matches

Domain ID domain_id	d3i9vd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.18 — HydB/Nqo4-like
Superfamily Superfamily superfamily	e.18.1 — HydB/Nqo4-like
Family Family family	e.18.1.2 — Nqo4-like

Domain ID domain_id	d3i9ve_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.307 — Nqo5-like
Superfamily Superfamily superfamily	d.307.1 — Nqo5-like
Family Family family	d.307.1.1 — Nqo5-like

Domain ID domain_id	d3i9vf_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.19 — HydA/Nqo6-like
Superfamily Superfamily superfamily	e.19.1 — HydA/Nqo6-like
Family Family family	e.19.1.2 — Nq06-like

Domain ID domain_id	d3i9vg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

Domain ID domain_id	d3i9vh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.82 — N domain of copper amine oxidase-like
Superfamily Superfamily superfamily	d.82.2 — Frataxin/Nqo15-like
Family Family family	d.82.2.2 — Nqo15-like

CATH v4.4 (20 domains)

Domain ID domain_id	3i9v101
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1450 —

Domain ID domain_id	3i9v102
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11540 — NADH-ubiquinone oxidoreductase 51kDa subunit

Domain ID domain_id	3i9v103
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	600 —

Domain ID domain_id	3i9v104
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	230 — NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain

Domain ID domain_id	3i9v201
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1590 — NADH-quinone oxidoreductase subunit E

Domain ID domain_id	3i9v202
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	3i9v400
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

Domain ID domain_id	3i9v600
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12280 —

Domain ID domain_id	3i9v700
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	920 — Metal Transport, Frataxin; Chain A
Homologous superfamily homologous superfamily	80 — NADH-quinone oxidoreductase, subunit 15

Domain ID domain_id	3i9v900
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3270 —

Domain ID domain_id	3i9vA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1450 —

Domain ID domain_id	3i9vA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11540 — NADH-ubiquinone oxidoreductase 51kDa subunit

Domain ID domain_id	3i9vA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	600 —

Domain ID domain_id	3i9vA04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	230 — NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain

Domain ID domain_id	3i9vB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1590 — NADH-quinone oxidoreductase subunit E

Domain ID domain_id	3i9vB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	3i9vD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

Domain ID domain_id	3i9vF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12280 —

Domain ID domain_id	3i9vG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3270 —

Domain ID domain_id	3i9vH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	920 — Metal Transport, Frataxin; Chain A
Homologous superfamily homologous superfamily	80 — NADH-quinone oxidoreductase, subunit 15

▶

Unit-cell length a length_a	108.963 Å
Unit-cell length b length_b	150.514 Å
Unit-cell length c length_c	216.726 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.19 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	29.935 Å
R factor r_factor	0.2360
R_work r_work	0.2350
R_free r_free	0.2830

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 2 mol/ASU

1. Protein Identity and Related Structures Protein Identity & Related Structures

NADH-quinone oxidoreductase subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit 6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit 9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NADH-quinone oxidoreductase subunit 15

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3i9v__assembly_1__model_1

3i9v__assembly_1__model_1 | I(q)

3i9v__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer