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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Aragao, D."

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Search Summary

This query matches 83 Structures.

Refinements

Structure Determination Methodology

experimental (83)

Scientific Name of Source Organism

	Homo sapiens (14)
	Mus musculus (14)
	Acinetobacter baumannii (7)
	Escherichia coli K-12 (7)
	Middle East respiratory syndrome-related coronavirus (7)
	Caldalkalibacillus thermarum TA2.A1 (6)
	Neisseria meningitidis (6)
	Brevibacillus brevis (4)
	Fusarium oxysporum f. sp. lycopersici (4)
	Hendra virus horse/Australia/Hendra/1994 (4)

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Taxonomy

	Bacteria (40)
	Eukaryota (32)
	Riboviria (16)
	Archaea (6)
	Duplodnaviria (3)
	Monodnaviria (3)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (83)

Polymer Entity Type

	Protein (83)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (11)
	1.5 - 2.0 (17)
	2.0 - 2.5 (31)
	2.5 - 3.0 (14)
	3.0 - 3.5 (5)
	3.5 - 4.0 (5)

Release Date

	2000 - 2004 (4)
	2005 - 2009 (3)
	2010 - 2014 (9)
	2015 - 2019 (42)
	2020 - 2024 (25)

Enzyme Classification Name

	Oxidoreductases (13)
	Hydrolases (9)
	Transferases (8)
	Translocases (2)

Membrane Protein Annotation

	MemProtMD (9)
	PDBTM (9)
	mpstruc (9)
	OPM (2)

Symmetry Type

	Asymmetric (38)
	Cyclic (26)
	Dihedral (18)
	Icosahedral (2)

SCOP Classification

	Alpha and beta proteins (a+b) (8)
	Membrane and cell surface proteins and peptides (6)
	All alpha proteins (12)
	Alpha and beta proteins (a/b) (4)
	Multi-domain proteins (alpha and beta) (4)
	Artifacts (2)
	All beta proteins (2)

AllSelected

1 to 25 of 83 Structures

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1GYO \| pdb_00001gyo	Download File View File

Crystal structure of the di-tetraheme cytochrome c3 from Desulfovibrio gigas at 1.2 Angstrom resolution

Aragao, D., Frazao, C., Sieker, L., Sheldrick, G.M., Legall, J., Carrondo, M.A.

(2003) Acta Crystallogr D Biol Crystallogr 59: 644

Released	2002-05-24
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Megalodesulfovibrio gigas
Macromolecule	CYTOCHROME C3, A DIMERIC CLASS III C-TYPE CYTOCHROME (protein)
Unique Ligands	GOL, HEC

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1OA0 \| pdb_00001oa0	Download File View File

REDUCED HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO DESULFURICANS X-RAY STRUCTURE AT 1.25A RESOLUTION

Macedo, S., Aragao, D., Mitchell, E.P., Romao, C.V., Liu, M.Y., Frazao, C., Saraiva, L.M., Xavier, A.V., Legall, J., Van Dongen, W.M.A.M., Hagen, W.R., Teixeira, M., Carrondo, M.A., Lindley, P.F.

(2003) J Biol Inorg Chem 8: 540-548

Released	2003-04-08
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Desulfovibrio desulfuricans
Macromolecule	PRISMANE PROTEIN (protein)
Unique Ligands	MES, SF3, SF4

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1OA1 \| pdb_00001oa1	Download File View File

REDUCED HYBRID CLUSTER PROTEIN (HCP) FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH STRUCTURE AT 1.55A RESOLUTION USING SYNCHROTRON RADIATION.

Aragao, D., Macedo, S., Mitchell, E.P., Romao, C.V., Liu, M.Y., Frazao, C., Saraiva, L.M., Xavier, A.V., Legall, J., Van Dongen, W.M.A.M., Hagen, W.R., Teixeira, M., Carrondo, M.A., Lindley, P.F.

(2003) J Biol Inorg Chem 8: 540

Released	2003-04-08
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Nitratidesulfovibrio vulgaris
Macromolecule	HYDROXYLAMINE REDUCTASE (protein)
Unique Ligands	GOL, SF3, SF4

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1UPX \| pdb_00001upx	Download File View File

The crystal structure of the Hybrid Cluster Protein from Desulfovibrio desulfuricans containing molecules in the oxidized and reduced states.

Aragao, D., Macedo, S., Mitchell, E.P., Lindley, P.F.

(2003) Acta Crystallogr D Biol Crystallogr 59: 2065

Released	2003-12-02
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Desulfovibrio desulfuricans
Macromolecule	HYDROXYLAMINE REDUCTASE (protein)
Unique Ligands	FSO, MES, SF3, SF4

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1W9M \| pdb_00001w9m	Download File View File

AS-isolated hybrid cluster protein from Desulfovibrio vulgaris X-ray structure at 1.35A resolution using iron anomalous signal

Aragao, D., Macedo, S., Mitchell, E.P., Coelho, D., Romao, C.V., Teixeira, M., Lindley, P.F.

(2008) Acta Crystallogr D Biol Crystallogr 64: 665

Released	2005-02-04
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Nitratidesulfovibrio vulgaris str. Hildenborough
Macromolecule	HYDROXYLAMINE REDUCTASE (protein)
Unique Ligands	FS2, SF4

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2UX8 \| pdb_00002ux8	Download File View File

Crystal Structure of Sphingomonas elodea ATCC 31461 Glucose-1- phosphate uridylyltransferase in Complex with glucose-1-phosphate.

Aragao, D., Fialho, A.M., Marques, A.R., Frazao, C., Sa-Correia, I., Mitchell, E.P.

(2007) J Bacteriol 189: 4520

Released	2007-05-22
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Sphingomonas elodea
Macromolecule	GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (protein)
Unique Ligands	G1P

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2VKR \| pdb_00002vkr	Download File View File

3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin

Frazao, C., Aragao, D., Coelho, R., Leal, S.S., Gomes, C.M., Teixeira, M., Carrondo, M.A.

(2008) FEBS Lett 582: 763-767

Released	2008-03-04
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Acidianus ambivalens
Macromolecule	ZINC-CONTAINING FERREDOXIN (protein)
Unique Ligands	F3S, SF4, ZN

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2XDC \| pdb_00002xdc	Download File View File

Structure of linear gramicidin D obtained using Type I crystals grown in a lipid cubic phase.

Hoefer, N., Aragao, D., Caffrey, M.

(2010) Biophys J 99: 23

Released	2010-08-11
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Brevibacillus brevis
Macromolecule	GRAMICIDIN A (protein)
Unique Ligands	15P, NA

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2Y5M \| pdb_00002y5m	Download File View File

STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 7.7 MONOACYLGLYCEROL LIPID CUBIC PHASE.

Hoefer, N., Aragao, D., Caffrey, M.

(2011) Cryst Growth Des 11: 1182

Released	2011-05-11
Method	X-RAY DIFFRACTION 1.08 Å
Organisms	Brevibacillus brevis
Macromolecule	VAL-GRAMICIDIN A (protein)
Unique Ligands	15P

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2Y6N \| pdb_00002y6n	Download File View File

STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 8.8 MONOACYLGLYCEROL LIPID CUBIC PHASE.

Hoefer, N., Aragao, D., Caffrey, M.

(2011) Cryst Growth Des 11: 1182

Released	2011-05-11
Method	X-RAY DIFFRACTION 1.26 Å
Organisms	Brevibacillus brevis
Macromolecule	VAL-GRAMICIDIN A (protein)
Unique Ligands	15P, P4C

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2YEV \| pdb_00002yev	Download File View File

Structure of caa3-type cytochrome oxidase

Lyons, J.A., Aragao, D., Soulimane, T., Caffrey, M.

(2012) Nature 487: 514

Released	2012-05-23
Method	X-RAY DIFFRACTION 2.36 Å
Organisms	Thermus thermophilus HB8
Macromolecule	CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV (protein) CYTOCHROME C OXIDASE POLYPEPTIDE I+III (protein) CYTOCHROME C OXIDASE SUBUNIT 2 (protein)
Unique Ligands	4AG, 5PL, 7E8, 7E9, CL, CU, CUA, HAS, HEC, MG

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3PDS \| pdb_00003pds	Download File View File

Irreversible Agonist-Beta2 Adrenoceptor Complex

Rosenbaum, D.M., Zhang, C., Lyons, J.A., Holl, R., Aragao, D., Arlow, D.H., Rasmussen, S.G.F., Choi, H.-J., DeVree, B.T., Sunahara, R.K., Chae, P.S., Gellman, S.H., Dror, R.O., Shaw, D.E., Weis, W.I., Caffrey, M., Gmeiner, P., Kobilka, B.K.

(2011) Nature 469: 236-240

Released	2011-01-12
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Fusion protein Beta-2 adrenergic receptor/Lysozyme (protein)
Unique Ligands	CLR, ERC, SO4

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3ZE3 \| pdb_00003ze3	Download File View File

Crystal structure of the integral membrane diacylglycerol kinase - delta7

Li, D., Pye, V.E., Lyons, J.A., Vogeley, L., Aragao, D., Caffrey, M.

(2013) Nature 497: 521

Released	2013-05-22
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Escherichia coli K-12
Macromolecule	DIACYLGLYCEROL KINASE (protein)
Unique Ligands	78M, 78N, ACT, FLC, NA, ZN

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3ZE4 \| pdb_00003ze4	Download File View File

Crystal structure of the integral membrane diacylglycerol kinase - wild-type

Li, D., Lyons, J.A., Pye, V.E., Vogeley, L., Aragao, D., Caffrey, M.

(2013) Nature 497: 521

Released	2013-05-22
Method	X-RAY DIFFRACTION 3.702 Å
Organisms	Escherichia coli K-12
Macromolecule	DIACYLGLYCEROL KINASE (protein)

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3ZE5 \| pdb_00003ze5	Download File View File

Crystal structure of the integral membrane diacylglycerol kinase - delta4

Li, D., Vogeley, L., Pye, V.E., Lyons, J.A., Aragao, D., Caffrey, M.

(2013) Nature 497: 521

Released	2013-05-22
Method	X-RAY DIFFRACTION 3.101 Å
Organisms	Escherichia coli K-12
Macromolecule	DIACYLGLYCEROL KINASE (protein)

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3ZQ8 \| pdb_00003zq8	Download File View File

STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A monovaccenin LIPID CUBIC PHASE

Hoefer, N., Aragao, D., Caffrey, M.

To be published

Released	2012-07-18
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Brevibacillus brevis
Macromolecule	VAL-GRAMICIDIN A (protein)
Unique Ligands	MVC

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4UXW \| pdb_00004uxw	Download File View File

Structure of delta4-DgkA-apo in 9.9 MAG

Li, D., Pye, V.E., Aragao, D., Caffrey, M.

(2015) Nat Commun 6: 10140

Released	2015-09-30
Method	X-RAY DIFFRACTION 3.15 Å
Organisms	Escherichia coli K-12
Macromolecule	DIACYLGLYCEROL KINASE (protein)
Unique Ligands	MPD, NA, NO3, OLC

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4UXX \| pdb_00004uxx	Download File View File

Structure of delta4-DgkA with AMPPCP in 9.9 MAG

Li, D., Vogeley, L., Caffrey, M.

(2015) Nat Commun 6: 10140

Released	2015-09-30
Method	X-RAY DIFFRACTION 2.701 Å
Organisms	Escherichia coli K-12
Macromolecule	DIACYLGLYCEROL KINASE (protein)
Unique Ligands	ACP, ACT, CL, MPD, NA, OLC, ZN

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4UXZ \| pdb_00004uxz	Download File View File

Structure of delta7-DgkA-syn in 7.9 MAG to 2.18 angstrom resolution

Li, D., Howe, N., Caffrey, M.

(2015) Nat Commun 6: 10140

Released	2015-09-30
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Escherichia coli K-12
Macromolecule	DIACYLGLYCEROL KINASE-DELTA 7 (protein)
Unique Ligands	79M, 79N, ACT, FLC, ZN

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4UYO \| pdb_00004uyo	Download File View File

Structure of delta7-DgkA in 7.9 MAG by serial femtosecond crystatallography to 2.18 angstrom resolution

Li, D., Howe, N., Other, O., Caffrey, M.

(2015) Nat Commun 6: 10140

Released	2015-09-30
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Escherichia coli K-12
Macromolecule	DIACYLGLYCEROL KINASE-DELTA 7 (protein)
Unique Ligands	79M, 79N, FLC, ZN

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4XCD \| pdb_00004xcd	Download File View File

Crystal structure of an octadecameric TF55 complex from S. solfataricus

Chaston, J.J., Stewart, A.G., Smits, C., Stock, D.

(2016) Structure 24: 364-374

Released	2016-02-10
Method	X-RAY DIFFRACTION 3.79 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	Thermosome subunit beta (protein)
Unique Ligands	ADP

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4XCG \| pdb_00004xcg	Download File View File

Crystal structure of a hexadecameric TF55 complex from S. solfataricus, crystal form I

Stewart, A.G., Smits, C., Chaston, J.J., Stock, D.

(2016) Structure 24: 364-374

Released	2016-02-10
Method	X-RAY DIFFRACTION 3.737 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	Thermosome subunit alpha (protein) Thermosome subunit beta (protein)
Unique Ligands	ADP

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4XCI \| pdb_00004xci	Download File View File

Crystal structure of a hexadecameric TF55 complex from S. solfataricus, crystal form II

Stewart, A.G., Chaston, J.J., Smits, C., Stock, D.

(2016) Structure 24: 364-374

Released	2016-02-10
Method	X-RAY DIFFRACTION 3.0023 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	Thermosome subunit alpha (protein) Thermosome subunit beta (protein)

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4ZRB \| pdb_00004zrb	Download File View File

Crystal Structure of Hypothetical Thioesterase Protein SP_1851 with Coenzyme A from Streptococcus pneumoniae TIGR4

Khandokar, Y.B., Srivastava, P., Forwood, J.K.

(2016) J Biological Chem 291: 1866-1876

Released	2015-05-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Streptococcus pneumoniae TIGR4
Macromolecule	Hypothetical Thioesterase Protein SP_1851 (protein)
Unique Ligands	COA

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5J09 \| pdb_00005j09	Download File View File

Crystal structure of decameric BFDV Capsid Protein

Sarker, S., Raidal, S., Aragao, D., Forwood, J.K.

(2016) Nat Commun 7: 13014-13014

Released	2016-05-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Beak and feather disease virus
Macromolecule	Beak and feather disease virus capsid protein (protein)

1 to 25 of 83 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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1GYO | pdb_00001gyo

1OA0 | pdb_00001oa0

1OA1 | pdb_00001oa1

1UPX | pdb_00001upx

1W9M | pdb_00001w9m

2UX8 | pdb_00002ux8

2VKR | pdb_00002vkr

2XDC | pdb_00002xdc

2Y5M | pdb_00002y5m

2Y6N | pdb_00002y6n

2YEV | pdb_00002yev

3PDS | pdb_00003pds

3ZE3 | pdb_00003ze3

3ZE4 | pdb_00003ze4

3ZE5 | pdb_00003ze5

3ZQ8 | pdb_00003zq8

4UXW | pdb_00004uxw

4UXX | pdb_00004uxx

4UXZ | pdb_00004uxz

4UYO | pdb_00004uyo

4XCD | pdb_00004xcd

4XCG | pdb_00004xcg

4XCI | pdb_00004xci

4ZRB | pdb_00004zrb

5J09 | pdb_00005j09