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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yu, Z."

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Search Summary

This query matches 115 Structures.

Refinements

Structure Determination Methodology

experimental (115)

Scientific Name of Source Organism

	Homo sapiens (54)
	Plasmodium vivax (9)
	Oryza sativa Japonica Group (6)
	Drosophila melanogaster (5)
	Human immunodeficiency virus 1 (5)
	Thermoplasma acidophilum (5)
	Escherichia coli (4)
	Oryza sativa (4)
	Salmonella enterica subsp. enterica serovar Typhimurium (4)
	synthetic construct (4)

More...

Taxonomy

	Eukaryota (89)
	Bacteria (17)
	Riboviria (12)
	Archaea (5)
	other sequences (4)
	Duplodnaviria (1)

Experimental Method

	ELECTRON MICROSCOPY (74)
	X-RAY DIFFRACTION (41)

Polymer Entity Type

	Protein (115)
	DNA (10)
	RNA (8)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (14)
	2.0 - 2.5 (17)
	2.5 - 3.0 (13)
	3.0 - 3.5 (26)
	3.5 - 4.0 (20)
	4.0 - 4.5 (11)
	> 4.5 (8)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (11)
	2015 - 2019 (34)
	2020 - 2024 (66)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (34)
	Transferases (30)
	Ligases (6)
	Oxidoreductases (4)
	Translocases (2)

Membrane Protein Annotation

	PDBTM (12)
	mpstruc (11)
	OPM (11)
	MemProtMD (10)

Symmetry Type

	Asymmetric (71)
	Cyclic (39)
	Dihedral (4)
	Helical (2)

SCOP Classification

	Alpha and beta proteins (a+b) (7)
	Artifacts (6)
	All alpha proteins (3)
	Alpha and beta proteins (a/b) (6)

AllSelected

1 to 25 of 115 Structures

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2GKS \| pdb_00002gks	Download File View File

Crystal Structure of the Bi-functional ATP Sulfurylase-APS Kinase from Aquifex aeolicus, a Chemolithotrophic Thermophile

Yu, Z., MacRea, I.J., Lansdon, E.B., Segel, I.H., Fisher, A.J.

(2007) J Mol Biology 365: 732-743

Released	2007-03-06
Method	X-RAY DIFFRACTION 2.31 Å
Organisms	Aquifex aeolicus
Macromolecule	Bifunctional SAT/APS kinase (protein)
Unique Ligands	ADP

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2OQ2 \| pdb_00002oq2	Download File View File

Crystal structure of yeast PAPS reductase with PAP, a product complex

Yu, Z., Fisher, A.J.

(2008) Biochemistry 47: 12777-12786

Released	2008-01-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Phosphoadenosine phosphosulfate reductase (protein)
Unique Ligands	A3P

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2WUU \| pdb_00002wuu	Download File View File

Structure of N-myristoyltransferase from L. donovani

Brannigan, J.A., Smith, B.A., Yu, Z., Hodgkinson, M.R., Leatherbarrow, R.J., Tate, E.W., Brzozowski, A.M., Smith, D.F., Wilkinson, A.J.

(2010) J Mol Biology 396: 985

Released	2009-12-01
Method	X-RAY DIFFRACTION 1.42 Å
Organisms	Leishmania donovani
Macromolecule	N-MYRISTOYLTRANSFERASE (protein)
Unique Ligands	NHW

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3J6C \| pdb_00003j6c	Download File View File

Cryo-EM structure of MAVS CARD filament

Xu, H., He, X., Zheng, H., Huang, L.J., Hou, F., Yu, Z., de la Cruz, M.J., Borkowski, B., Zhang, X., Chen, Z.J., Jiang, Q.-X.

(2014) Elife 3: e01489-e01489

Released	2014-03-05
Method	ELECTRON MICROSCOPY 9.6 Å
Organisms	Homo sapiens
Macromolecule	Mitochondrial antiviral-signaling protein (protein)

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3MOW \| pdb_00003mow	Download File View File

Crystal structure of SHP2 in complex with a tautomycetin analog TTN D-1

Zhang, Z.-Y., Liu, S., Yu, Z., Yu, X.

To be published

Released	2011-05-04
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein phosphatase non-receptor type 11 (protein)
Unique Ligands	B2B

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3O5X \| pdb_00003o5x	Download File View File

Crystal structure of the oncogenic tyrosine phosphatase SHP2 complexed with a salicylic acid-based small molecule inhibitor

Zhang, Z.-Y., Zhang, X., He, Y., Liu, S., Yu, Z., Jiang, Z., Yang, Z., Dong, Y., Nabinger, S.C., Wu, L., Gunawan, A.M., Wang, L., Chan, R.J.

(2010) J Med Chem 53: 2482-2493

Released	2010-08-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein phosphatase non-receptor type 11 (protein)
Unique Ligands	JZG

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4B10 \| pdb_00004b10	Download File View File

Plasmodium vivax N-myristoyltransferase with a non-hydrolysable co- factor

Yu, Z., Brannigan, J.A., Moss, D.K., Brzozowski, A.M., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2012) J Med Chem 55: 8879

Released	2012-10-17
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Plasmodium vivax
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	CL, DMS, MG, NHW, SO4

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4B11 \| pdb_00004b11	Download File View File

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 13)

Yu, Z., Brannigan, J.A., Moss, D.K., Brzozowski, A.M., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2012) J Med Chem 55: 8879

Released	2012-10-17
Method	X-RAY DIFFRACTION 1.59 Å
Organisms	Plasmodium vivax
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	7I1, CL, DMS, MG, NHW, SO4

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4B12 \| pdb_00004b12	Download File View File

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23)

Yu, Z., Brannigan, J.A., Moss, D.K., Brzozowski, A.M., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2012) J Med Chem 55: 8879

Released	2012-10-17
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Plasmodium vivax
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	C23, CL, DMS, MG, NHW, SO4

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4B13 \| pdb_00004b13	Download File View File

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 25)

Yu, Z., Brannigan, J.A., Moss, D.K., Brzozowski, A.M., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2012) J Med Chem 55: 8879

Released	2012-10-17
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Plasmodium vivax
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	CL, MG, NHW, SO4, X25

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4B14 \| pdb_00004b14	Download File View File

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 26)

Yu, Z., Brannigan, J.A., Moss, D.K., Brzozowski, A.M., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2012) J Med Chem 55: 8879

Released	2012-10-17
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Plasmodium vivax
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	4XB, CL, DMS, MG, NHW, SO4

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4BBH \| pdb_00004bbh	Download File View File

Plasmodium vivax N-myristoyltransferase with a bound benzothiophene inhibitor

Rackham, M.D., Brannigan, J.A., Moss, D.K., Yu, Z., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2013) J Med Chem 56: 371

Released	2012-12-05
Method	X-RAY DIFFRACTION 1.63 Å
Organisms	Plasmodium vivax
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	CL, DMS, MG, NHW, SO4, YBN

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4JS9 \| pdb_00004js9	Download File View File

Structural Characterization of Inducible Nitric Oxide Synthase Substituted With Mesoheme

Hannibal, L., Page, R.C., Bolisetty, K., Yu, Z., Misra, S., Stuehr, D.J.

To be published

Released	2014-04-23
Method	X-RAY DIFFRACTION 2.784 Å
Organisms	Mus musculus
Macromolecule	Nitric oxide synthase, inducible (protein)
Unique Ligands	H4B, MH0, SO4

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4OWP \| pdb_00004owp	Download File View File

Crystal structure of rpn11 in a heterodimer complex with rpn8, representing the active portion of the proteasome lid.

Yu, Z., Mansour, W., Nakasone, M.A., Glickman, M.H., Dvir, H.

To be published

Released	2015-08-05
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	26S proteasome regulatory subunit RPN11 (protein) 26S proteasome regulatory subunit RPN8 (protein)
Unique Ligands	ZN

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4PKM \| pdb_00004pkm	Download File View File

Crystal Structure of Bacillus thuringiensis Cry51Aa1 Protoxin at 1.65 Angstroms Resolution

Xu, C., Chinte, U., Chen, L., Yao, Q., Zhou, D., Meng, Y., Li, L., Rose, J., Bi, L.J., Yu, Z., Sun, M., Wang, B.C.

(2015) Biochem Biophys Res Commun 462: 184-189

Released	2015-06-03
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Bacillus thuringiensis F14-1
Macromolecule	Cry51Aa1 (protein)
Unique Ligands	GLY, GOL, SO4

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4PVG \| pdb_00004pvg	Download File View File

Crystal structure of protein tyrosine phosphatase Shp2 catalytic domain complex with small molecular compound L88N79

Zhang, Z.-Y., Zeng, L., Liu, D., Yu, Z.

To be published

Released	2015-04-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein phosphatase non-receptor type 11 (protein)
Unique Ligands	2WT

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4QQN \| pdb_00004qqn	Download File View File

Protein arginine methyltransferase 3 in complex with compound MTV044246

Dong, A., Dobrovetsky, E., Tempel, W., He, H., Zhao, K., Smil, D., Landon, M., Luo, X., Chen, Z., Dai, M., Yu, Z., Lin, Y., Zhang, H., Zhao, K., Schapira, M., Brown, P.J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Vedadi, M., Structural Genomics Consortium (SGC)

(2018) J Med Chem 61: 1204-1217

Released	2014-09-17
Method	X-RAY DIFFRACTION 2.08 Å
Organisms	Homo sapiens
Macromolecule	PRMT3 protein (protein)
Unique Ligands	3BQ, CL, GOL, UNX

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4RYL \| pdb_00004ryl	Download File View File

Human Protein Arginine Methyltransferase 3 in complex with 1-isoquinolin-6-yl-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea

Dong, A., Dobrovetsky, E., Kaniskan, H.U., Szewczyk, M., Yu, Z., Eram, M.S., Yang, X., Schmidt, K., Luo, X., Dai, M., He, F., Zang, I., Lin, Y., Kennedy, S., Li, F., Tempel, W., Smil, D., Min, S.J., Landon, M., Lin-Jones, J., Huang, X.P., Roth, B.L., Schapira, M., Atadja, P., Barsyte-Lovejoy, D., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Zhao, K., Jin, J., Vedadi, M., Structural Genomics Consortium (SGC)

(2015) Angew Chem Int Ed Engl 54: 5166-5170

Released	2015-02-25
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	PRMT3 protein (protein)
Unique Ligands	3ZG, UNX

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4UFV \| pdb_00004ufv	Download File View File

Plasmodium vivax N-myristoyltransferase in complex with a pyridyl inhibitor (compound 18)

Yu, Z., Brannigan, J.A., Rangachari, K., Heal, W.P., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2015) Medchemcomm 6: 1767

Released	2016-02-03
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Plasmodium vivax
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	31A, CL, DMS, GOA, MG, NHW, SO4

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4UFW \| pdb_00004ufw	Download File View File

Plasmodium vivax N-myristoyltransferase in complex with a pyridyl inhibitor (compound 22)

Yu, Z., Brannigan, J.A., Rangachari, K., Heal, W.P., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2015) Medchemcomm 6: 1767

Released	2016-02-03
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Plasmodium vivax
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	7Y6, CL, DMS, MG, NHW, SO4

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4UFX \| pdb_00004ufx	Download File View File

Plasmodium vivax N-myristoyltransferase in complex with a pyridyl inhibitor (compound 19)

Yu, Z., Brannigan, J.A., Rangachari, K., Heal, W.P., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2015) Medchemcomm 6: 1767

Released	2016-02-03
Method	X-RAY DIFFRACTION 1.49 Å
Organisms	Plasmodium vivax
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	80O, CL, DMS, MG, NHW, SO4

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5A27 \| pdb_00005a27	Download File View File

Leishmania major N-myristoyltransferase in complex with a chlorophenyl 1,2,4-oxadiazole inhibitor.

Rackham, M.D., Yu, Z., Brannigan, J.A., Heal, W.P., Paape, D., Barker, K.V., Wilkinson, A.J., Smith, D.F., Tate, E.W., Leatherbarrow, R.J.

(2015) Medchemcomm 6: 1761

Released	2016-03-23
Method	X-RAY DIFFRACTION 1.37 Å
Organisms	Leishmania major
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	MG, MYA, TUT

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5A28 \| pdb_00005a28	Download File View File

Leishmania major N-myristoyltransferase in complex with a chlorophenyl 1,3,4-oxadiazole inhibitor.

Rackham, M.D., Yu, Z., Brannigan, J.A., Heal, W.P., Paape, D., Barker, K.V., Wilkinson, A.J., Smith, D.F., Tate, E.W., Leatherbarrow, R.J.

(2015) Medchemcomm 6: 1761

Released	2016-03-23
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Leishmania major
Macromolecule	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE (protein)
Unique Ligands	MG, MYA, TUQ

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5CD7 \| pdb_00005cd7	Download File View File

Crystal structure of the NTD L199M of Drosophila Oskar protein

Yang, N., Hu, M., Yu, Z., Wang, M., Lehmann, R., Xu, R.M.

(2015) Proc Natl Acad Sci U S A 112: 11541-11546

Released	2015-09-02
Method	X-RAY DIFFRACTION 2.502 Å
Organisms	Drosophila melanogaster
Macromolecule	Maternal effect protein oskar (protein)
Unique Ligands	GOL

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5CD8 \| pdb_00005cd8	Download File View File

Crystal structure of the NTD of Drosophila Oskar protein

Yang, N., Hu, M., Yu, Z., Wang, M., Lehmann, R., Xu, R.M.

(2015) Proc Natl Acad Sci U S A 112: 11541-11546

Released	2015-09-02
Method	X-RAY DIFFRACTION 3.001 Å
Organisms	Drosophila melanogaster
Macromolecule	Maternal effect protein oskar (protein)
Unique Ligands	GOL

1 to 25 of 115 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

2GKS | pdb_00002gks

2OQ2 | pdb_00002oq2

2WUU | pdb_00002wuu

3J6C | pdb_00003j6c

3MOW | pdb_00003mow

3O5X | pdb_00003o5x

4B10 | pdb_00004b10

4B11 | pdb_00004b11

4B12 | pdb_00004b12

4B13 | pdb_00004b13

4B14 | pdb_00004b14

4BBH | pdb_00004bbh

4JS9 | pdb_00004js9

4OWP | pdb_00004owp

4PKM | pdb_00004pkm

4PVG | pdb_00004pvg

4QQN | pdb_00004qqn

4RYL | pdb_00004ryl

4UFV | pdb_00004ufv

4UFW | pdb_00004ufw

4UFX | pdb_00004ufx

5A27 | pdb_00005a27

5A28 | pdb_00005a28

5CD7 | pdb_00005cd7

5CD8 | pdb_00005cd8