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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Deng, X."

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Search Summary

This query matches 72 Structures.

Refinements

Structure Determination Methodology

experimental (72)

Scientific Name of Source Organism

	Plasmodium falciparum 3D7 (30)
	Homo sapiens (16)
	Escherichia coli (5)
	Staphylococcus aureus (5)
	Staphylococcus delphini (5)
	Prosthecobacter vanneervenii (2)
	Acinetobacter baumannii (1)
	Campylobacter jejuni subsp. jejuni 81116 (1)
	Drosophila melanogaster (1)
	Francisella tularensis subsp. novicida (1)

More...

Taxonomy

	Eukaryota (51)
	Bacteria (27)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (63)
	ELECTRON MICROSCOPY (9)

Polymer Entity Type

	Protein (72)
	RNA (8)
	DNA (3)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (11)
	2.0 - 2.5 (24)
	2.5 - 3.0 (11)
	3.0 - 3.5 (17)
	3.5 - 4.0 (4)
	4.0 - 4.5 (1)

Release Date

	2005 - 2009 (6)
	2010 - 2014 (15)
	2015 - 2019 (19)
	2020 - 2024 (21)
	2025 - 2029 (11)

Enzyme Classification Name

	Oxidoreductases (33)
	Hydrolases (12)
	Ligases (4)
	Transferases (3)
	Lyases (2)

Membrane Protein Annotation

	mpstruc (10)
	OPM (1)

Symmetry Type

	Asymmetric (60)
	Cyclic (13)
	Helical (1)

SCOP Classification

	Alpha and beta proteins (a/b) (20)
	All beta proteins (4)
	Artifacts (6)
	All alpha proteins (2)
	Alpha and beta proteins (a+b) (4)

AllSelected

1 to 25 of 72 Structures

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2PI2 \| pdb_00002pi2	Download File View File

Full-length Replication protein A subunits RPA14 and RPA32

Deng, X., Borgstahl, G.E.

(2007) J Mol Biology 374: 865-876

Released	2007-10-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Replication protein A 14 kDa subunit (protein) Replication protein A 32 kDa subunit (protein)
Unique Ligands	DIO

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2PQA \| pdb_00002pqa	Download File View File

Crystal Structure of Full-length Human RPA 14/32 Heterodimer

Deng, X., Borgstahl, G.E.

(2007) J Mol Biology 374: 865-876

Released	2007-11-13
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Replication protein A 14 kDa subunit (protein) Replication protein A 32 kDa subunit (protein)

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2Z6K \| pdb_00002z6k	Download File View File

Crystal structure of full-length human RPA14/32 heterodimer

Deng, X., Habel, J.E., Kabaleeswaran, V., Borgstahl, G.E.

(2007) J Mol Biology 374: 865-876

Released	2007-12-04
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Replication protein A 14 kDa subunit (protein) Replication protein A 32 kDa subunit (protein)

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3I65 \| pdb_00003i65	Download File View File

Plasmodium falciparum dihydroorotate dehydrogenase bound with triazolopyrimidine-based inhibitor DSM1

Deng, X., Phillips, M.A.

(2009) J Biological Chem 284: 26999-27009

Released	2009-07-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Dihydroorotate dehydrogenase homolog, mitochondrial (protein)
Unique Ligands	FMN, JZ8, LDA, ORO

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3I68 \| pdb_00003i68	Download File View File

Plasmodium falciparum dihydroorotate dehydrogenase bound with triazolopyrimidine-based inhibitor DSM2

Deng, X., Phillips, M.A.

(2009) J Biological Chem 284: 26999-27009

Released	2009-07-28
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Dihydroorotate dehydrogenase homolog, mitochondrial (protein)
Unique Ligands	FMN, J4Z, ORO

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3I6R \| pdb_00003i6r	Download File View File

Plasmodium falciparum dihydroorotate dehydrogenase bound with triazolopyrimidine-based inhibitor DSM74

Deng, X., Phillips, M.A.

(2009) J Biological Chem 284: 26999-27009

Released	2009-07-28
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Dihydroorotate dehydrogenase homolog, mitochondrial (protein)
Unique Ligands	FMN, J5Z, ORO

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3N29 \| pdb_00003n29	Download File View File

Crystal structure of carboxynorspermidine decarboxylase complexed with Norspermidine from Campylobacter jejuni

Deng, X., Lee, J., Michael, A.J., Tomchick, D.R., Goldsmith, E.J., Phillips, M.A.

(2010) J Biological Chem 285: 25708-25719

Released	2010-06-09
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Campylobacter jejuni subsp. jejuni 81116
Macromolecule	Carboxynorspermidine decarboxylase (protein)
Unique Ligands	GOL, NSD, PLP

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3N2O \| pdb_00003n2o	Download File View File

X-ray crystal structure of arginine decarboxylase complexed with Arginine from Vibrio vulnificus

Deng, X., Lee, J., Michael, A.J., Tomchick, D.R., Goldsmith, E.J., Phillips, M.A.

(2010) J Biological Chem 285: 25708-25719

Released	2010-06-09
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Vibrio vulnificus YJ016
Macromolecule	Biosynthetic arginine decarboxylase (protein)
Unique Ligands	AG2, PLP

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3O8A \| pdb_00003o8a	Download File View File

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with novel Inhibitor Genz667348

Deng, X., Booker, M.L., Phillips, M.A.

(2010) J Biological Chem 285: 33054-33064

Released	2010-08-18
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Dihydroorotate dehydrogenase homolog, mitochondrial (protein)
Unique Ligands	FMN, LDA, O8A, ORO

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3S84 \| pdb_00003s84	Download File View File

Dimeric apoA-IV

Deng, X., Davidson, W.S., Thompson, T.B.

(2012) Structure 20: 767-779

Released	2012-05-16
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Apolipoprotein A-IV (protein)
Unique Ligands	SO4

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3SFK \| pdb_00003sfk	Download File View File

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM267

Deng, X., Phillips, M.

(2011) J Med Chem 54: 5540-5561

Released	2011-07-06
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Dihydroorotate dehydrogenase (quinone), mitochondrial (protein)
Unique Ligands	D67, FMN, ORO

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4B99 \| pdb_00004b99	Download File View File

Crystal Structure of MAPK7 (ERK5) with inhibitor

Elkins, J.M., Wang, J., Vollmar, M., Mahajan, P., Savitsky, P., Deng, X., Gray, N.S., Pike, A.C.W., von Delft, F., Bountra, C., Arrowsmith, C., Edwards, A., Knapp, S.

(2013) J Med Chem 56: 4413

Released	2012-09-19
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	MITOGEN-ACTIVATED PROTEIN KINASE 7 (protein)
Unique Ligands	R4L

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4CC5 \| pdb_00004cc5	Download File View File

Fragment-Based Discovery of 6 Azaindazoles As Inhibitors of Bacterial DNA Ligase

Howard, S., Amin, N., Benowitz, A.B., Chiarparin, E., Cui, H., Deng, X., Heightman, T.D., Holmes, D.J., Hopkins, A., Huang, J., Jin, Q., Kreatsoulas, C., Martin, A.C.L., Massey, F., McCloskey, L., Mortenson, P.N., Pathuri, P., Tisi, D., Williams, P.A.

(2013) ACS Med Chem Lett 4: 1208

Released	2014-06-18
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Staphylococcus aureus
Macromolecule	DNA LIGASE (protein)
Unique Ligands	L5V, SO4

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4CC6 \| pdb_00004cc6	Download File View File

Fragment-Based Discovery of 6 Azaindazoles As Inhibitors of Bacterial DNA Ligase

(2013) ACS Med Chem Lett 4: 1208

Released	2014-06-18
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Staphylococcus aureus
Macromolecule	DNA LIGASE (protein)
Unique Ligands	L5Y, SO4

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4GXO \| pdb_00004gxo	Download File View File

Crystal structure of Staphylococcus aureus protein SarZ mutant C13E

Sun, F., Ding, Y., Ji, Q., Liang, Z., Deng, X., Wong, C.C., Yi, C., Zhang, L., Xie, S., Alvarez, S., Hicks, L.M., Luo, C., Jiang, H., Lan, L., He, C.

(2012) Proc Natl Acad Sci U S A 109: 15461-15466

Released	2012-09-26
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Staphylococcus aureus subsp. aureus str. Newman
Macromolecule	MarR family regulatory protein (protein)
Unique Ligands	GOL

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4HQM \| pdb_00004hqm	Download File View File

The crystal structure of QsrR-menadione complex

Ji, Q., Zhang, L., Jones, M.B., Sun, F., Deng, X., Liang, H., Brugarolas, P., Gao, N., Peterson, S.N., Lan, L., Bae, T., He, C.

(2013) Proc Natl Acad Sci U S A 110: 5010-5015

Released	2013-03-06
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Staphylococcus aureus
Macromolecule	QsrR protein (protein)
Unique Ligands	17Z

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4IGH \| pdb_00004igh	Download File View File

High resolution crystal structure of human dihydroorotate dehydrogenase bound with 4-quinoline carboxylic acid analog

Deng, X., Das, P., Fontoura, B.M.A., Phillips, M.A., De Brabander, J.K.

(2013) ACS Med Chem Lett 4: 517-521

Released	2013-08-21
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Homo sapiens
Macromolecule	Dihydroorotate dehydrogenase (quinone), mitochondrial (protein)
Unique Ligands	1EA, FMN, GOL, ORO, ZWI

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4JPH \| pdb_00004jph	Download File View File

Crystal structure of Protein Related to DAN and Cerberus (PRDC)

Deng, X., Nolan, K.T., Kattamuri, C., Thompson, T.B.

(2013) Structure 21: 1417-1429

Released	2013-07-24
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Mus musculus
Macromolecule	Gremlin-2 (protein)
Unique Ligands	CIT, GOL, GSH

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4OQV \| pdb_00004oqv	Download File View File

High resolution crystal structure of human dihydroorotate dehydrogenase bound with DSM338 (N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine)

Deng, X., Phillips, M.A.

(2014) J Med Chem 57: 5381-5394

Released	2014-06-04
Method	X-RAY DIFFRACTION 1.23 Å
Organisms	Homo sapiens
Macromolecule	Dihydroorotate dehydrogenase (quinone), mitochondrial (protein)
Unique Ligands	2V6, ACY, FMN, GOL, NA, ORO, SO4

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4ORI \| pdb_00004ori	Download File View File

Rat dihydroorotate dehydrogenase bound with DSM338 (N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine)

Deng, X., Phillips, M.A.

(2014) J Med Chem 57: 5381-5394

Released	2014-06-04
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Rattus norvegicus
Macromolecule	Dihydroorotate dehydrogenase (quinone), mitochondrial (protein)
Unique Ligands	2V6, FMN, ORO

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4ORM \| pdb_00004orm	Download File View File

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM338 (N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine)

Deng, X., Phillips, M.A.

(2014) J Med Chem 57: 5381-5394

Released	2014-06-04
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Dihydroorotate dehydrogenase (quinone), mitochondrial (protein)
Unique Ligands	2V6, FMN, GOL, ORO, SO4

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4Q2V \| pdb_00004q2v	Download File View File

Crystal Structure of Ricin A chain complexed with Baicalin inhibitor

Deng, X., Li, X., Dong, J., Chen, Y.

(2015) J Biological Chem 290: 12899-12907

Released	2015-04-15
Method	X-RAY DIFFRACTION 2.198 Å
Organisms	Ricinus communis
Macromolecule	Ricin (protein)
Unique Ligands	0XE

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4QEI \| pdb_00004qei	Download File View File

Two distinct conformational states of GlyRS captured in crystal lattice

Xie, W., Qin, X., Deng, X., Zhang, Q., Li, Q.

(2016) J Biological Chem 291: 5740-5752

Released	2015-05-20
Method	X-RAY DIFFRACTION 2.875 Å
Organisms	Homo sapiens
Macromolecule	Glycine--tRNA ligase (protein) tRNA-Gly-CCC-2-2 (nucleic acid)
Unique Ligands	AMP

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4RX0 \| pdb_00004rx0	Download File View File

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM265

Deng, X., Phillips, M., Tomchick, D.

(2015) Sci Transl Med 7: 296ra111-296ra111

Released	2015-07-29
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Dihydroorotate dehydrogenase (quinone), mitochondrial (protein)
Unique Ligands	D65, FMN, GOL, ORO

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5BOO \| pdb_00005boo	Download File View File

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM265

Phillips, M., Deng, X., Tomchick, D.

(2015) Sci Transl Med 7: 296ra111-296ra111

Released	2015-07-29
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Dihydroorotate dehydrogenase (quinone), mitochondrial (protein)
Unique Ligands	D65, FMN, ORO

1 to 25 of 72 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

2PI2 | pdb_00002pi2

2PQA | pdb_00002pqa

2Z6K | pdb_00002z6k

3I65 | pdb_00003i65

3I68 | pdb_00003i68

3I6R | pdb_00003i6r

3N29 | pdb_00003n29

3N2O | pdb_00003n2o

3O8A | pdb_00003o8a

3S84 | pdb_00003s84

3SFK | pdb_00003sfk

4B99 | pdb_00004b99

4CC5 | pdb_00004cc5

4CC6 | pdb_00004cc6

4GXO | pdb_00004gxo

4HQM | pdb_00004hqm

4IGH | pdb_00004igh

4JPH | pdb_00004jph

4OQV | pdb_00004oqv

4ORI | pdb_00004ori

4ORM | pdb_00004orm

4Q2V | pdb_00004q2v

4QEI | pdb_00004qei

4RX0 | pdb_00004rx0

5BOO | pdb_00005boo