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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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Search Summary

This query matches 22 Structures.

Refinements

Structure Determination Methodology

experimental (22)

Scientific Name of Source Organism

	Azotobacter vinelandii (3)
	Homo sapiens (3)
	Severe acute respiratory syndrome coronavirus 2 (3)
	Acidithiobacillus ferrooxidans ATCC 23270 (1)
	Amblyomma virus GXTV108 (1)
	Aquifex aeolicus (1)
	Dictyostelium discoideum (1)
	Escherichia coli BL21(DE3) (1)
	Eubacterium barkeri (1)
	Leptotrichia wadei F0279 (1)

More...

Taxonomy

	Bacteria (13)
	Eukaryota (5)
	Riboviria (3)
	unclassified viruses (1)

Experimental Method

X-RAY DIFFRACTION (22)

Polymer Entity Type

Protein (22)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (7)
	2.0 - 2.5 (7)
	2.5 - 3.0 (4)
	3.0 - 3.5 (1)
	4.0 - 4.5 (1)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (3)
	2010 - 2014 (4)
	2015 - 2019 (4)
	2020 - 2024 (10)

Enzyme Classification Name

	Hydrolases (7)
	Oxidoreductases (8)
	Transferases (3)

Symmetry Type

	Cyclic (14)
	Asymmetric (6)
	Dihedral (2)
	Helical (1)

SCOP Classification

	Alpha and beta proteins (a/b) (4)
	Multi-domain proteins (alpha and beta) (1)
	Alpha and beta proteins (a+b) (3)
	All alpha proteins (2)
	Artifacts (3)
	All beta proteins (2)

AllSelected

1 to 22 of 22 Structures

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1PAE \| pdb_00001pae	Download File View File

nucleoside diphosphate kinase

Strub, M.-P., Hoh, F., Sanchez, J.-F., Strub, J.M., Bock, A., Aumelas, A., Dumas, C.

(2003) Structure 11: 1359-1367

Released	2003-11-11
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Dictyostelium discoideum
Macromolecule	Nucleoside diphosphate kinase, cytosolic (protein)
Unique Ligands	SE

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2ARH \| pdb_00002arh	Download File View File

Crystal Structure of a Protein of Unknown Function AQ1966 from Aquifex aeolicus VF5

Qiu, Y., Kim, Y., Yang, X., Collart, F., Joachimiak, A., Kossiakoff, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2005-10-04
Method	X-RAY DIFFRACTION 2.46 Å
Organisms	Aquifex aeolicus
Macromolecule	hypothetical protein aq_1966 (protein)
Unique Ligands	CA, SE, SO4

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2GJ8 \| pdb_00002gj8	Download File View File

Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and K+

Scrima, A., Wittinghofer, A.

(2006) EMBO J 25: 2940-2951

Released	2006-07-04
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli BL21(DE3)
Macromolecule	tRNA modification GTPase trmE (protein)
Unique Ligands	ALF, GDP, K, MG, SE

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3HRD \| pdb_00003hrd	Download File View File

Crystal structure of nicotinate dehydrogenase

Wagener, N., Pierik, A.J., Hille, R., Dobbek, H.

(2009) Proc Natl Acad Sci U S A 106: 11055-11060

Released	2009-06-30
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Eubacterium barkeri
Macromolecule	Nicotinate dehydrogenase FAD-subunit (protein) Nicotinate dehydrogenase large molybdopterin subunit (protein) Nicotinate dehydrogenase medium molybdopterin subunit (protein) Nicotinate dehydrogenase small FeS subunit (protein)
Unique Ligands	CA, FAD, FES, MCN, MG, MOS, NIO, NO3, SE

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3RJ1 \| pdb_00003rj1	Download File View File

Architecture of the Mediator Head module

Imasaki, T., Calero, G., Cai, G., Tsai, K.L., Yamada, K., Cardelli, F., Erdjument-Bromage, H., Tempst, P., Berger, I., Kornberg, G.L., Asturias, F.J., Kornberg, R.D., Takagi, Y.

(2011) Nature 475: 240-243

Released	2011-07-27
Method	X-RAY DIFFRACTION 4.3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 7
Unique Ligands	SE

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3SZ0 \| pdb_00003sz0	Download File View File

Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans in complex with sodium selenide

Cherney, M.M., Zhang, Y., James, M.N.G., Weiner, J.H.

(2012) J Struct Biol 178: 319-328

Released	2012-05-16
Method	X-RAY DIFFRACTION 2.1501 Å
Organisms	Acidithiobacillus ferrooxidans ATCC 23270
Macromolecule	Sulfide-quinone reductase, putative (protein)
Unique Ligands	6SE, FAD, LMT, SE, SO4

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3UHJ \| pdb_00003uhj	Download File View File

Crystal structure of a probable glycerol dehydrogenase from Sinorhizobium meliloti 1021

Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

To be published

Released	2011-11-23
Method	X-RAY DIFFRACTION 2.34 Å
Organisms	Sinorhizobium meliloti
Macromolecule	Probable glycerol dehydrogenase (protein)
Unique Ligands	GOL, SE, ZN

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4CJ9 \| pdb_00004cj9	Download File View File

BurrH DNA-binding protein from Burkholderia rhizoxinica in its apo form

Stella, S., Molina, R., Lopez-Mendez, B., Campos-Olivas, R., Duchateau, P., Montoya, G.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2042

Released	2014-07-09
Method	X-RAY DIFFRACTION 2.214 Å
Organisms	Mycetohabitans rhizoxinica
Macromolecule	BURRH (protein)
Unique Ligands	SE

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5BVG \| pdb_00005bvg	Download File View File

Selenium incorporated nitrogenase MoFe-protein (Av1-Se2B) from A. vinelandii

Spatzal, T., Perez, K.A., Howard, J.B., Rees, D.C.

(2015) Elife 4: e11620-e11620

Released	2015-12-30
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Azotobacter vinelandii
Macromolecule	Nitrogenase molybdenum-iron protein alpha chain (protein) Nitrogenase molybdenum-iron protein beta chain (protein)
Unique Ligands	CL, CLF, FE2, HCA, ICG, IMD, SE

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5FF4 \| pdb_00005ff4	Download File View File

HydE from T. maritima in complex with (2R,4R)-TMeTDA

Rohac, R., Amara, P., Benjdia, A., Martin, L., Ruffie, P., Favier, A., Berteau, O., Mouesca, J.M., Fontecilla-Camps, J.C., Nicolet, Y.

(2016) Nat Chem 8: 491-500

Released	2016-04-06
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Thermotoga maritima
Macromolecule	[FeFe] hydrogenase maturase subunit HydE (protein)
Unique Ligands	5ZZ, CL, CPS, SAH, SE, SFS

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6OP2 \| pdb_00006op2	Download File View File

Selenium incorporated FeMo-cofactor of nitrogenase from azotobacter vinelandii at high concentration of selenium

Arias, R.J., Rees, D.C.

(2019) J Am Chem Soc 141: 13676-13688

Released	2019-08-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Azotobacter vinelandii
Macromolecule	Nitrogenase molybdenum-iron protein alpha chain (protein) Nitrogenase molybdenum-iron protein beta chain (protein)
Unique Ligands	CA, CLF, HCA, ICS, IMD, MG, SE

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6OP3 \| pdb_00006op3	Download File View File

Selenium incorporated FeMo-cofactor of nitrogenase from Azotobacter vinelandii with low concentration of selenium

Arias, R.J., Rees, D.C.

(2019) J Am Chem Soc 141: 13676-13688

Released	2019-08-14
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Azotobacter vinelandii
Macromolecule	Nitrogenase molybdenum-iron protein alpha chain (protein) Nitrogenase molybdenum-iron protein beta chain (protein)
Unique Ligands	CA, CLF, HCA, ICS, IMD, MG, SE

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7BAK \| pdb_00007bak	Download File View File

Crystal structure of SARS-CoV-2 main protease treated with ebselen

Amporndanai, K., O'Neill, P.M., Hasnain, S.S.

(2021) Nat Commun 12: 3061-3061

Released	2021-06-02
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Main Protease (protein)
Unique Ligands	SE

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7BAL \| pdb_00007bal	Download File View File

Crystal structure of SARS-CoV-2 main protease treated with ebselen derivative of MR6-31-2

Amporndanai, K., O'Neill, P.M., Hasnain, S.S.

(2021) Nat Commun 12: 3061-3061

Released	2021-06-02
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Main Protease (protein)
Unique Ligands	SE

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7T8G \| pdb_00007t8g	Download File View File

G93A mutant of human SOD1 bound with MR6-8-2 in P21 space group

Amporndanai, K., Hasnain, S.S.

(2024) Sci Rep 14: 12118-12118

Released	2023-01-25
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Homo sapiens
Macromolecule	Superoxide dismutase [Cu-Zn] (protein)
Unique Ligands	ACT, Q8H, SE, SO4, ZN

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7W9G \| pdb_00007w9g	Download File View File

Complex structure of Mpro with ebselen-derivative inhibitor

Sahoo, P., Kumar, A.

(2023) Acs Pharmacol Transl Sci 6: 171-180

Released	2022-12-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	3C-like proteinase nsp5 (protein)
Unique Ligands	SE

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7XMW \| pdb_00007xmw	Download File View File

Crystal structure of anti-CRISPR protein AcrVIA2

Yan, X., Li, X., Song, G.

(2022) Biochem Biophys Res Commun 612: 84-90

Released	2023-05-31
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Leptotrichia wadei F0279
Macromolecule	AcrVIA2 (protein)
Unique Ligands	PE4, SE, ZN

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7ZCY \| pdb_00007zcy	Download File View File

Sporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms

Mazzei, L., Ciurli, S., Cianci, M.

(2023) J Med Chem 66: 2054-2063

Released	2023-04-19
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Sporosarcina pasteurii
Macromolecule	Urease subunit alpha (protein) Urease subunit beta (protein) Urease subunit gamma (protein)
Unique Ligands	EDO, IU9, NI, OH, SE, SO4

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8WU2 \| pdb_00008wu2	Download File View File

Crystal structure of RNA-dependent RNA polymerases from Jingmen tick virus

Liu, Z., Han, P., Peng, Q., Qi, J.

(2024) Hlife 2: 18-31

Released	2024-02-07
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Amblyomma virus GXTV108
Macromolecule	RNA polymerase (protein)
Unique Ligands	SE

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8YD7 \| pdb_00008yd7	Download File View File

Structure of FADD/Caspase-8/cFLIP death effector domain assembly

Lin, S.-C., Yang, C.-Y.

(2024) Nat Commun 15: 3791-3791

Released	2024-05-15
Method	X-RAY DIFFRACTION 3.32 Å
Organisms	Homo sapiens
Macromolecule	CASP8 and FADD-like apoptosis regulator subunit p12 (protein) Caspase-8 (protein) FAS-associated death domain protein (protein)
Unique Ligands	SE

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8YM4 \| pdb_00008ym4	Download File View File

Structure of Caspase-8/cFLIP death effector domain assembly

Lin, S.-C., Yang, C.-Y.

(2024) Nat Commun 15: 8974-8974

Released	2024-10-30
Method	X-RAY DIFFRACTION 2.34 Å
Organisms	Homo sapiens
Macromolecule	CASP8 and FADD-like apoptosis regulator subunit p43 (protein) Caspase-8 (protein)
Unique Ligands	SE

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8YOU \| pdb_00008you	Download File View File

The pmTcDH complex structure with an inhibitor SeCN

Varfolomeeva, L.A., Polyakov, K.M., Shipkov, N.S., Dergousova, N.I., Boyko, K.M., Tikhonova, T.V., Popov, V.O.

To be published

Released	2024-03-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pelomicrobium methylotrophicum
Macromolecule	Twin-arginine translocation signal domain-containing protein (protein)
Unique Ligands	CU, GOL, NA, SE, SEK

1 to 22 of 22 Structures

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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

1PAE | pdb_00001pae

2ARH | pdb_00002arh

2GJ8 | pdb_00002gj8

3HRD | pdb_00003hrd

3RJ1 | pdb_00003rj1

3SZ0 | pdb_00003sz0

3UHJ | pdb_00003uhj

4CJ9 | pdb_00004cj9

5BVG | pdb_00005bvg

5FF4 | pdb_00005ff4

6OP2 | pdb_00006op2

6OP3 | pdb_00006op3

7BAK | pdb_00007bak

7BAL | pdb_00007bal

7T8G | pdb_00007t8g

7W9G | pdb_00007w9g

7XMW | pdb_00007xmw

7ZCY | pdb_00007zcy

8WU2 | pdb_00008wu2

8YD7 | pdb_00008yd7

8YM4 | pdb_00008ym4

8YOU | pdb_00008you