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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 2.7.4.11

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Search Summary

This query matches 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	Saccharomyces cerevisiae S288C (10)
	Plasmodium falciparum 3D7 (3)
	Pseudomonas aeruginosa PAO1 (3)
	Mycolicibacterium smegmatis MC2 155 (2)
	Staphylococcus aureus (1)
	Staphylococcus aureus subsp. aureus NCTC 8325 (1)

Taxonomy

	Eukaryota (13)
	Bacteria (7)

Experimental Method

	X-RAY DIFFRACTION (18)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

Protein (20)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (9)
	2.5 - 3.0 (5)
	3.0 - 3.5 (5)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (7)
	2015 - 2019 (9)
	2025 - 2029 (2)

Enzyme Classification Name

Oxidoreductases (20)

Membrane Protein Annotation

	mpstruc (7)
	OPM (2)

Symmetry Type

	Cyclic (18)
	Asymmetric (4)

AllSelected

1 to 20 of 20 Structures

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2GJL \| pdb_00002gjl	Download File View File

Crystal Structure of 2-nitropropane dioxygenase

Suh, S.W.

(2006) J Biological Chem 281: 18660-18667

Released	2006-05-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	hypothetical protein PA1024 (protein)
Unique Ligands	FMN

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2GJN \| pdb_00002gjn	Download File View File

crystal structure of 2-nitropropane dioxygenase complexed with FMN and substrate

Suh, S.W.

(2006) J Biological Chem 281: 18660-18667

Released	2006-05-16
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	hypothetical protein PA1024 (protein)
Unique Ligands	FMN, NIS

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4G6G \| pdb_00004g6g	Download File View File

Crystal structure of NDH with TRT

Li, W., Feng, Y., Ge, J., Yang, M.

(2012) Nature 491: 478-482

Released	2012-10-24
Method	X-RAY DIFFRACTION 2.39 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (protein)
Unique Ligands	FAD, MG, TRT

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4G6H \| pdb_00004g6h	Download File View File

Crystal structure of NDH with NADH

Li, W., Feng, Y., Ge, J., Yang, M.

(2012) Nature 491: 478-482

Released	2012-10-24
Method	X-RAY DIFFRACTION 2.262 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (protein)
Unique Ligands	FAD, MG, NAI

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4G73 \| pdb_00004g73	Download File View File

Crystal structure of NDH with NADH and Quinone

Li, W., Feng, Y., Ge, J., Yang, M.

(2012) Nature 491: 478-482

Released	2012-10-24
Method	X-RAY DIFFRACTION 2.522 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (protein)
Unique Ligands	FAD, MG, NAI, UQ5

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4G74 \| pdb_00004g74	Download File View File

Crystal structure of NDH with Quinone

Li, W., Feng, Y., Ge, J., Yang, M.

(2012) Nature 491: 478-482

Released	2012-10-24
Method	X-RAY DIFFRACTION 2.48 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (protein)
Unique Ligands	FAD, MG, TRT, UQ5

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4G9K \| pdb_00004g9k	Download File View File

Structure of the Ndi1 protein from Saccharomyces cerevisiae

Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A.D., Maher, M.J.

(2012) Proc Natl Acad Sci U S A 109: 15247-15252

Released	2012-09-05
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Rotenone-insensitive NADH-ubiquinone oxidoreductase (protein)
Unique Ligands	FAD

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4GAP \| pdb_00004gap	Download File View File

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with NAD+

Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A.D., Maher, M.J.

(2012) Proc Natl Acad Sci U S A 109: 15247-15252

Released	2012-09-05
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Rotenone-insensitive NADH-ubiquinone oxidoreductase (protein)
Unique Ligands	FAD, NAD

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4GAV \| pdb_00004gav	Download File View File

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with quinone

Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A.D., Maher, M.J.

(2012) Proc Natl Acad Sci U S A 109: 15247-15252

Released	2012-09-05
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Rotenone-insensitive NADH-ubiquinone oxidoreductase (protein)
Unique Ligands	FAD, UQ2

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5JWA \| pdb_00005jwa	Download File View File

the structure of malaria PfNDH2

Yu, Y., Yang, Y.Q., Li, X.L., Yu, J., Ge, J.P., Li, J., Rao, Y., Yang, M.J.

(2017) J Med Chem 60: 1994-2005

Released	2017-03-22
Method	X-RAY DIFFRACTION 2.162 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	NADH dehydrogenase, putative (protein)
Unique Ligands	ACT, FAD, MG, TRT

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5JWB \| pdb_00005jwb	Download File View File

Structure of NDH2 from plasmodium falciparum in complex with NADH

Yu, Y., Li, X.L.

(2017) J Med Chem 60: 1994-2005

Released	2017-03-29
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Type II NADH:ubiquinone oxidoreductase (protein)
Unique Ligands	ACT, CXS, FAD, MG, NAD, TRT

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5JWC \| pdb_00005jwc	Download File View File

Structure of NDH2 from plasmodium falciparum in complex with RYL-552

Yu, Y.

(2017) J Med Chem 60: 1994-2005

Released	2017-03-22
Method	X-RAY DIFFRACTION 2.051 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	NADH dehydrogenase, putative (protein)
Unique Ligands	4W0, FAD, MG, TRT

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5NA1 \| pdb_00005na1	Download File View File

NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein structure - 2.32 A resolution

Brito, J.A., Athayde, D., Sousa, F.M., Sena, F.V., Pereira, M.M., Archer, M.

(2017) Biochim Biophys Acta 1858: 823-832

Released	2018-01-10
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	Staphylococcus aureus subsp. aureus NCTC 8325
Macromolecule	NADH dehydrogenase-like protein SAOUHSC_00878 (protein)
Unique Ligands	FAD, MLI, PO4

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5NA4 \| pdb_00005na4	Download File View File

NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - E172S mutant

Brito, J.A., Athayde, D., Sousa, F.M., Sena, F.V., Pereira, M.M., Archer, M.

(2017) Biochim Biophys Acta 1858: 823-832

Released	2018-01-10
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Staphylococcus aureus
Macromolecule	NADH dehydrogenase-like protein SAOUHSC_00878 (protein)
Unique Ligands	FAD

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5YJW \| pdb_00005yjw	Download File View File

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with the competitive inhibitor, stigmatellin.

Yamasita, T., Inaoka, D.K., Shiba, T., Oohashi, T., Iwata, S., Yagi, T., Kosaka, H., Harada, S., Kita, K., Hirano, K.

(2018) Sci Rep 8: 2427-2427

Released	2018-02-14
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (protein)
Unique Ligands	FAD, GOL, MES, MG, P6G, PE4, PEG, PG4, PGE, SMA

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5YJX \| pdb_00005yjx	Download File View File

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with myxothiazol.

Yamasita, T., Inaoka, D.K., Shiba, T., Oohashi, T., Iwata, S., Yagi, T., Kosaka, H., Harada, S., Kita, K., Hirano, K.

(2018) Sci Rep 8: 2427-2427

Released	2018-02-14
Method	X-RAY DIFFRACTION 3.21 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (protein)
Unique Ligands	FAD, MES, MG, MYX

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5YJY \| pdb_00005yjy	Download File View File

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with AC0-12.

Yamasita, T., Inaoka, D.K., Shiba, T., Oohashi, T., Iwata, S., Yagi, T., Kosaka, H., Harada, S., Kita, K., Hirano, K.

(2018) Sci Rep 8: 2427-2427

Released	2018-02-14
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (protein)
Unique Ligands	8WF, FAD, MES, MG

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6E2A \| pdb_00006e2a	Download File View File

Crystal structure of NADH:quinone reductase PA1024 from Pseudomonas aeruginosa PAO1 in complex with NAD+

Reis, R.A.G., Ball, J., Agniswamy, J., Weber, I., Gadda, G.

(2019) Protein Sci 28: 167-175

Released	2019-02-06
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	Nitronate monooxygenase (protein)
Unique Ligands	FMN, GOL, NAD

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9MQY \| pdb_00009mqy	Download File View File

Structure of mycobacterial NDH2 (type II NADH:quinone oxidoreductase)

Liang, Y., Rubinstein, J.L.

To be published

Released	2025-01-22
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	NADH:ubiquinone reductase (non-electrogenic) (protein)
Unique Ligands	FAD

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9MQZ \| pdb_00009mqz	Download File View File

Structure of mycobacterial NDH2 (type II NADH:quinone oxidoreductase) with 2-mercapto-quinazolinone inhibitor.

Liang, Y., Rubinstein, J.L.

To be published

Released	2025-01-22
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	NADH:ubiquinone reductase (non-electrogenic) (protein)
Unique Ligands	A1BNR, FAD

1 to 20 of 20 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

2GJL | pdb_00002gjl

Crystal Structure of 2-nitropropane dioxygenase

2GJN | pdb_00002gjn

crystal structure of 2-nitropropane dioxygenase complexed with FMN and substrate

4G6G | pdb_00004g6g

Crystal structure of NDH with TRT

4G6H | pdb_00004g6h

Crystal structure of NDH with NADH

4G73 | pdb_00004g73

Crystal structure of NDH with NADH and Quinone

4G74 | pdb_00004g74

Crystal structure of NDH with Quinone

4G9K | pdb_00004g9k

Structure of the Ndi1 protein from Saccharomyces cerevisiae

4GAP | pdb_00004gap

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with NAD+

4GAV | pdb_00004gav

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with quinone

5JWA | pdb_00005jwa

the structure of malaria PfNDH2

5JWB | pdb_00005jwb

Structure of NDH2 from plasmodium falciparum in complex with NADH

5JWC | pdb_00005jwc

Structure of NDH2 from plasmodium falciparum in complex with RYL-552

5NA1 | pdb_00005na1

NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein structure - 2.32 A resolution

5NA4 | pdb_00005na4

NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - E172S mutant

5YJW | pdb_00005yjw

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with the competitive inhibitor, stigmatellin.

5YJX | pdb_00005yjx

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with myxothiazol.

5YJY | pdb_00005yjy

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with AC0-12.

6E2A | pdb_00006e2a

Crystal structure of NADH:quinone reductase PA1024 from Pseudomonas aeruginosa PAO1 in complex with NAD+

9MQY | pdb_00009mqy

Structure of mycobacterial NDH2 (type II NADH:quinone oxidoreductase)

9MQZ | pdb_00009mqz

Structure of mycobacterial NDH2 (type II NADH:quinone oxidoreductase) with 2-mercapto-quinazolinone inhibitor.

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

2GJL | pdb_00002gjl

2GJN | pdb_00002gjn

4G6G | pdb_00004g6g

4G6H | pdb_00004g6h

4G73 | pdb_00004g73

4G74 | pdb_00004g74

4G9K | pdb_00004g9k

4GAP | pdb_00004gap

4GAV | pdb_00004gav

5JWA | pdb_00005jwa

5JWB | pdb_00005jwb

5JWC | pdb_00005jwc

5NA1 | pdb_00005na1

5NA4 | pdb_00005na4

5YJW | pdb_00005yjw

5YJX | pdb_00005yjx

5YJY | pdb_00005yjy

6E2A | pdb_00006e2a

9MQY | pdb_00009mqy

9MQZ | pdb_00009mqz