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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Popov, V.O."

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Search Summary

This query matches 178 Structures.

Refinements

Structure Determination Methodology

experimental (178)

Scientific Name of Source Organism

	Thioalkalivibrio nitratireducens (20)
	Thioalkalivibrio paradoxus ARh 1 (14)
	Pyrobaculum ferrireducens (9)
	Aminobacterium colombiense (8)
	Pelomicrobium methylotrophicum (8)
	Haliscomenobacter hydrossis DSM 1100 (7)
	Bombyx mori (5)
	Drosophila melanogaster (5)
	Entacmaea quadricolor (4)
	Pseudomonas sp. 101 (4)

More...

Taxonomy

	Bacteria (114)
	Eukaryota (35)
	Archaea (24)
	other sequences (4)
	Duplodnaviria (3)
	Riboviria (2)
	unclassified sequences (2)

Experimental Method

	X-RAY DIFFRACTION (175)
	SOLUTION NMR (2)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (178)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (20)
	1.5 - 2.0 (83)
	2.0 - 2.5 (49)
	2.5 - 3.0 (17)
	3.0 - 3.5 (5)
	3.5 - 4.0 (1)

Release Date

	1995 - 1999 (2)
	2005 - 2009 (10)
	2010 - 2014 (42)
	2015 - 2019 (38)
	2020 - 2024 (83)
	2025 - 2029 (3)

Enzyme Classification Name

	Oxidoreductases (44)
	Transferases (23)
	Hydrolases (13)
	Ligases (2)

Symmetry Type

	Cyclic (83)
	Asymmetric (45)
	Dihedral (54)
	Tetrahedral (1)

SCOP Classification

	Alpha and beta proteins (a/b) (18)
	Multi-domain proteins (alpha and beta) (8)
	Artifacts (8)
	Alpha and beta proteins (a+b) (7)
	All alpha proteins (3)
	Membrane and cell surface proteins and peptides (1)

AllSelected

1 to 25 of 178 Structures

Page 1 of 8

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2GO1 \| pdb_00002go1	Download File View File

NAD-dependent formate dehydrogenase from Pseudomonas sp.101

Filippova, E.V., Polyakov, K.M., Tikhonova, T.V., Stekhanova, T.N., Boiko, K.M., Popov, V.O.

(2005) Crystallogr Rep 50: 796-800

Released	2006-05-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Pseudomonas sp. 101
Macromolecule	NAD-dependent formate dehydrogenase (protein)
Unique Ligands	SO4

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2GSD \| pdb_00002gsd	Download File View File

NAD-dependent formate dehydrogenase from bacterium Moraxella sp.C2 in complex with NAD and azide

Filippova, E.V., Polyakov, K.M., Tikhonova, T.V., Sadykhov, I.G., Shabalin, I.G., Tishkov, V.I., Popov, V.O.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1315-1325

Released	2006-05-09
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Moraxella sp.
Macromolecule	NAD-dependent formate dehydrogenase (protein)
Unique Ligands	AZI, NAD

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2GUG \| pdb_00002gug	Download File View File

NAD-dependent formate dehydrogenase from Pseudomonas sp.101 in complex with formate

Filippova, E.V., Polyakov, K.M., Tikhonova, T.V., Boiko, K.M., Tishkov, V.I., Popov, V.O.

(2006) Кристаллография 51: 663-667

Released	2006-05-16
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Pseudomonas sp. 101
Macromolecule	Formate dehydrogenase (protein)
Unique Ligands	FMT, PEG, PG4

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2NAC \| pdb_00002nac	Download File View File

HIGH RESOLUTION STRUCTURES OF HOLO AND APO FORMATE DEHYDROGENASE

Lamzin, V.S., Dauter, Z., Popov, V.O., Harutyunyan, E.H., Wilson, K.S.

(1994) J Mol Biology 236: 759-785

Released	1995-01-26
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas sp. 101
Macromolecule	NAD-DEPENDENT FORMATE DEHYDROGENASE (protein)
Unique Ligands	SO4

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2NAD \| pdb_00002nad	Download File View File

HIGH RESOLUTION STRUCTURES OF HOLO AND APO FORMATE DEHYDROGENASE

Lamzin, V.S., Dauter, Z., Popov, V.O., Harutyunyan, E.H., Wilson, K.S.

(1994) J Mol Biology 236: 759-785

Released	1995-01-26
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Pseudomonas sp. 101
Macromolecule	NAD-DEPENDENT FORMATE DEHYDROGENASE (protein)
Unique Ligands	AZI, NAD, SO4

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2NDP \| pdb_00002ndp	Download File View File

Structure of DNA-binding HU protein from micoplasma Mycoplasma gallisepticum

Altukhov, D.A., Talyzina, A.A., Agapova, Y.K., Vlaskina, A.V., Korzhenevskiy, D.A., Bocharov, E.V., Rakitina, T.V., Timofeev, V.I., Popov, V.O.

(2018) J Biomol Struct Dyn 36: 45-53

Released	2016-11-09
Method	SOLUTION NMR
Organisms	Mycoplasmoides gallisepticum S6
Macromolecule	Histone-like DNA-binding superfamily protein (protein)

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2OT4 \| pdb_00002ot4	Download File View File

Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio nitratireducens

Polyakov, K.M., Boyko, K.M., Slutsky, A., Tikhonova, T.V., Antipov, A.N., Zvyagilskaya, R.A., Popov, A.N., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

(2009) J Mol Biology 389: 846-862

Released	2008-04-08
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	CA, CIT, HEC, MPD, MRD

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2ZO5 \| pdb_00002zo5	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with azide

Polyakov, K.M., Boyko, K.M., Slutsky, A., Tikhonova, T.V., Antipov, A.N., Zvyagilskaya, R.A., Popov, A.N., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

(2009) J Mol Biology 389: 846-862

Released	2009-05-05
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	AZI, CA, HEC, NA, PG4, PG6, TRS

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3D1I \| pdb_00003d1i	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite

Polyakov, K.M., Boyko, K.M., Slutsky, A., Tikhonova, T.V., Antipov, A.N., Zvyagilskaya, R.A., Popov, A.N., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

(2009) J Mol Biology 389: 846-862

Released	2009-05-12
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	CA, HEC, NA, NO2, PG4, PG6

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3F29 \| pdb_00003f29	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with sulfite

Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Slutsky, A., Tikhonova, T.V., Antipov, A.N., Zvyagilskaya, R.A., Popov, A.N., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

To be published

Released	2008-12-09
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	CA, HEC, PG4, PG6, SO3

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3FN4 \| pdb_00003fn4	Download File View File

Apo-form of NAD-dependent formate dehydrogenase from bacterium Moraxella sp.C-1 in closed conformation

Shabalin, I.G., Polyakov, K.M., Filippova, E.V., Dorovatovskiy, P.V., Tikhonova, T.V., Sadykhov, E.G., Tishkov, V.I., Popov, V.O.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1315-1325

Released	2009-12-01
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Moraxella sp.
Macromolecule	NAD-dependent formate dehydrogenase (protein)
Unique Ligands	GOL, SO4

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3FO3 \| pdb_00003fo3	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)

Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Slutsky, A., Tikhonova, T.V., Antipov, A.N., Zvyagilskaya, R.A., Popov, A.N., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

(2010) Acta Crystallogr D Biol Crystallogr 66: 1043-1047

Released	2009-12-29
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	ACT, CA, HEC, NA, PG4, PG6, SO3, SO4, THJ, TRS

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3GM6 \| pdb_00003gm6	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with phosphate

Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Filimonenkov, A.A., Dorovatovsky, P.V., Tikhonova, T.V., Popov, V.O.

(2010) Crystallogr Rep 55: 58-64

Released	2009-08-04
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	CA, HEC, MPD, MRD, PO4

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3JTM \| pdb_00003jtm	Download File View File

Structure of recombinant formate dehydrogenase from Arabidopsis thaliana

Timofeev, V.I., Shabalin, I.G., Serov, A.E., Polyakov, K.M., Popov, V.O., Tishkov, V.I., Kuranova, I.P., Samigina, V.R.

To be published

Released	2010-09-15
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Arabidopsis thaliana
Macromolecule	Formate dehydrogenase, mitochondrial (protein)
Unique Ligands	AZI, GOL, SO4

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3LG1 \| pdb_00003lg1	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium borohydride (in complex with sulfite)

Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Filimonenkov, A.A., Dorovatovsky, P.V., Tikhonova, T.V., Popov, V.O.

(2012) Acta Crystallogr D Biol Crystallogr 68: 144-153

Released	2010-12-29
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	CA, HEC, NA, PG4, PG6, SO3

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3LGQ \| pdb_00003lgq	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with sulfite (modified Tyr-303)

Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Filimonenkov, A.A., Tikhonova, T.V., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

(2012) Acta Crystallogr D Biol Crystallogr 68: 144-153

Released	2011-02-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	CA, HEC, MPD, SO3, TRS

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3MMO \| pdb_00003mmo	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with cyanide

Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Tikhonova, T.V., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

(2010) Acta Crystallogr D Biol Crystallogr 66: 1043-1047

Released	2010-09-29
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	CA, CYN, HEC, NA, PG4, PG6, TRS

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3N7U \| pdb_00003n7u	Download File View File

NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex with NAD and azide

Shabalin, I.G., Polyakov, K.M., Serov, A.E., Skirgello, O.E., Sadykhov, E.G., Dorovatovskiy, P.V., Tishkov, V.I., Popov, V.O.

To be published

Released	2010-06-09
Method	X-RAY DIFFRACTION 2 Å
Organisms	Arabidopsis thaliana
Macromolecule	Formate dehydrogenase (protein)
Unique Ligands	AZI, GOL, NAD, SO4

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3NAQ \| pdb_00003naq	Download File View File

Apo-form of NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana

Shabalin, I.G., Polyakov, K.M., Serov, A.E., Skirgello, O.E., Sadykhov, E.G., Dorovatovskiy, P.V., Tishkov, V.I., Popov, V.O.

To be published

Released	2010-07-07
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Arabidopsis thaliana
Macromolecule	Formate dehydrogenase (protein)
Unique Ligands	SO4

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3OWM \| pdb_00003owm	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with hydroxylamine

Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Tikhonova, T.V., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

To be published

Released	2011-10-26
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	CA, HEC, NA, NO2, PG4, PG6, TRS

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3RKH \| pdb_00003rkh	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite (full occupancy)

Trofimov, A.A., Polyakov, K.M., Tikhonova, T.V., Tikhonov, A.V., Dorovatovskii, P.V., Popov, V.O.

(2012) Acta Crystallogr D Biol Crystallogr 68: 144-153

Released	2011-06-15
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	CA, HEC, MRD, NO2

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3RR5 \| pdb_00003rr5	Download File View File

DNA ligase from the archaeon Thermococcus sp. 1519

Petrova, T., Bezsudnova, E.Y., Boyko, K.M., Mardanov, A.V., Popov, V.O., Polyakov, K.M., Ravin, N.V., Shabalin, I.G., Skryabin, K.G., Stekhanova, T.N., Kovalchuk, M.V.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1440-1447

Released	2012-04-11
Method	X-RAY DIFFRACTION 3.018 Å
Organisms	Thermococcus sp. 1519
Macromolecule	DNA ligase (protein)
Unique Ligands	MG

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3S7W \| pdb_00003s7w	Download File View File

Structure of the TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with an oxidized Gln360 in a complex with hydroxylamine

Trofimov, A.A., Polyakov, K.M., Tikhonova, T.V., Popov, V.O.

To be published

Released	2011-07-27
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	AZI, CA, GOL, HEC, NO2

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3SCE \| pdb_00003sce	Download File View File

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with a covalent bond between the CE1 atom of Tyr303 and the CG atom of Gln360 (TvNiRb)

Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Tikhonova, T.V., Popov, V.O.

(2012) Acta Crystallogr D Biol Crystallogr 68: 144-153

Released	2011-07-06
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Thioalkalivibrio nitratireducens
Macromolecule	Eight-heme nitrite reductase (protein)
Unique Ligands	CA, HEC, NA, PG4, PG6, PO4

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3SQR \| pdb_00003sqr	Download File View File

Crystal structure of laccase from Botrytis aclada at 1.67 A resolution

Osipov, E.M., Polyakov, K.M., Tikhonova, T.V., Dorovatovsky, P.V., Ludwig, R., Kittl, R., Shleev, S.V., Popov, V.O.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2913-2923

Released	2012-07-11
Method	X-RAY DIFFRACTION 1.67 Å
Organisms	Botrytis aclada
Macromolecule	laccase (protein)
Unique Ligands	CU, MAN, NAG, SO4
Unique branched monosaccharides	BMA, MAN, NAG

1 to 25 of 178 Structures

Page 1 of 8

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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

Symmetry Type

SCOP Classification

2GO1 | pdb_00002go1

2GSD | pdb_00002gsd

2GUG | pdb_00002gug

2NAC | pdb_00002nac

2NAD | pdb_00002nad

2NDP | pdb_00002ndp

2OT4 | pdb_00002ot4

2ZO5 | pdb_00002zo5

3D1I | pdb_00003d1i

3F29 | pdb_00003f29

3FN4 | pdb_00003fn4

3FO3 | pdb_00003fo3

3GM6 | pdb_00003gm6

3JTM | pdb_00003jtm

3LG1 | pdb_00003lg1

3LGQ | pdb_00003lgq

3MMO | pdb_00003mmo

3N7U | pdb_00003n7u

3NAQ | pdb_00003naq

3OWM | pdb_00003owm

3RKH | pdb_00003rkh

3RR5 | pdb_00003rr5

3S7W | pdb_00003s7w

3SCE | pdb_00003sce

3SQR | pdb_00003sqr