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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ye, J."

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Search Summary

This query matches 75 Structures.

Refinements

Structure Determination Methodology

experimental (75)

Scientific Name of Source Organism

	Homo sapiens (43)
	Mus musculus (9)
	Komagataella pastoris (7)
	Neisseria gonorrhoeae (7)
	Escherichia coli (5)
	Neisseria gonorrhoeae FA 1090 (4)
	Escherichia coli K-12 (2)
	Rattus norvegicus (2)
	Archaeoglobus fulgidus DSM 4304 (1)
	Lama glama (1)

More...

Taxonomy

	Eukaryota (53)
	Bacteria (21)
	Archaea (1)
	Duplodnaviria (1)
	Riboviria (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (48)
	ELECTRON MICROSCOPY (24)
	SOLUTION NMR (3)

Polymer Entity Type

	Protein (75)
	DNA (3)
	RNA (1)

Refinement Resolution (Å)

	0.5 - 1.0 (2)
	1.0 - 1.5 (8)
	1.5 - 2.0 (17)
	2.0 - 2.5 (12)
	2.5 - 3.0 (5)
	3.0 - 3.5 (19)
	3.5 - 4.0 (9)

Release Date

	2000 - 2004 (6)
	2005 - 2009 (3)
	2010 - 2014 (10)
	2015 - 2019 (6)
	2020 - 2024 (50)

Enzyme Classification Name

	Hydrolases (9)
	Transferases (25)
	Translocases (7)
	Oxidoreductases (2)

Membrane Protein Annotation

	PDBTM (21)
	MemProtMD (13)
	mpstruc (17)
	OPM (2)

Symmetry Type

	Asymmetric (54)
	Cyclic (19)
	Dihedral (2)

SCOP Classification

	All beta proteins (3)
	Alpha and beta proteins (a+b) (12)
	Alpha and beta proteins (a/b) (4)
	Small proteins (1)
	Artifacts (7)
	All alpha proteins (4)
	Membrane and cell surface proteins and peptides (3)

AllSelected

1 to 25 of 75 Structures

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1G2S	Download File View File

SOLUTION STRUCTURE OF EOTAXIN-3

Ye, J., Mayer, K.L., Mayer, M.R., Stone, M.J.

(2001) Biochemistry 40: 7820-7831

Released	2002-03-13
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	EOTAXIN-3 (protein)

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1G2T	Download File View File

SOLUTION STRUCTURE OF EOTAXIN-3

Ye, J., Mayer, K.L., Mayer, M.R., Stone, M.J.

(2001) Biochemistry 40: 7820-7831

Released	2002-03-13
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	EOTAXIN-3 (protein)

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1HTV	Download File View File

CRYSTAL STRUCTURE OF DESTRIPEPTIDE (B28-B30) INSULIN

Ye, J., Chang, W., Liang, D.

(2001) Biochim Biophys Acta 1547: 18-25

Released	2001-05-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	INSULIN (protein)
Unique Ligands	ZN

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1TLW	Download File View File

Tsx structure complexed with thymidine

Ye, J., van den Berg, B.

(2004) EMBO J 23: 3187-3195

Released	2004-08-24
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Escherichia coli
Macromolecule	Nucleoside-specific channel-forming protein tsx (protein)
Unique Ligands	THM

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1TLY	Download File View File

Tsx structure

Ye, J., van den Berg, B.

(2004) EMBO J 23: 3187-3195

Released	2004-08-24
Method	X-RAY DIFFRACTION 3.01 Å
Organisms	Escherichia coli
Macromolecule	Nucleoside-specific channel-forming protein tsx (protein)

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1TLZ	Download File View File

Tsx structure complexed with uridine

Ye, J., van den Berg, B.

(2004) EMBO J 23: 3187-3195

Released	2004-08-24
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Escherichia coli
Macromolecule	Nucleoside-specific channel-forming protein tsx (protein)
Unique Ligands	URI

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1U2W	Download File View File

Crystal Structure of the Staphylococcus aureus pI258 CadC

Ye, J., Kandegedara, A., Martin, P., Rosen, B.P.

(2005) J Bacteriol 187: 4214-4221

Released	2005-07-12
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Staphylococcus aureus
Macromolecule	Cadmium efflux system accessory protein (protein)
Unique Ligands	ZN

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2N4X	Download File View File

Structure of the Transmembrane Electron Transporter CcdA

Chou, J.J., Williamson, J.A.

(2015) Nat Struct Mol Biol 22: 809-814

Released	2016-05-18
Method	SOLUTION NMR
Organisms	Archaeoglobus fulgidus DSM 4304
Macromolecule	Cytochrome C-type biogenesis protein (CcdA) (protein)

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2PPT	Download File View File

Crystal structure of thioredoxin-2

Ye, J., Chou, S., Beckwith, J., Rapoport, T.

To be published

Released	2007-10-02
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Rhodobacter capsulatus
Macromolecule	thioredoxin-2 (protein)
Unique Ligands	ZN

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2Q62	Download File View File

Crystal Structure of ArsH from Sinorhizobium meliloti

Ye, J., Yang, H., Bhattacharjee, H., Rosen, B.P.

(2007) FEBS Lett 581: 3996-4000

Released	2007-12-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Sinorhizobium meliloti
Macromolecule	arsH (protein)
Unique Ligands	SO4

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3IVK	Download File View File

Crystal Structure of the Catalytic Core of an RNA Polymerase Ribozyme Complexed with an Antigen Binding Antibody Fragment

Koldobskaya, Y., Duguid, E.M., Shechner, D.M., Koide, S., Kossiakoff, A.A., Bartel, D.P., Piccirilli, J.A.

(2009) Science 326: 1271-1275

Released	2010-03-02
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Mus musculus
Macromolecule	Fab heavy chain (protein) Fab light chain (protein) class I ligase product (nucleic acid)
Unique Ligands	CD, CL, MG

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3KGK	Download File View File

Crystal structure of ArsD

Ye, J., Rosen, B.P.

(2010) Biochemistry 49: 5206-5212

Released	2010-02-16
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Escherichia coli
Macromolecule	Arsenical resistance operon trans-acting repressor arsD (protein)

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3KOV	Download File View File

Structure of MEF2A bound to DNA reveals a completely folded MADS-box/MEF2 domain that recognizes DNA and recruits transcription co-factors

Wu, Y., Dey, R., Han, A., Jayathilaka, N., Philips, M., Ye, J., Chen, L.

(2010) J Mol Biol 397: 520-533

Released	2010-02-16
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	Myocyte-specific enhancer factor 2A (protein) DNA (5'-D(APAPCPTPAPTPTPTPAPTPAPAPG)-3') (nucleic acid) DNA (5'-D(TPCPTPTPAPTPAPAPAPTPAPGPT)-3') (nucleic acid)

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3MU6	Download File View File

Inhibiting the Binding of Class IIa Histone Deacetylases to Myocyte Enhancer Factor-2 by Small Molecules

Jayathilaka, N., Han, A., Gaffney, K., Dey, R., He, J., Ye, J., Gao, T., Petasis, N.A., Chen, L.

(2012) Nucleic Acids Res 40: 5378-5388

Released	2011-11-02
Method	X-RAY DIFFRACTION 2.434 Å
Organisms	Homo sapiens
Macromolecule	Myocyte-specific enhancer factor 2A (protein) DNA (5'-D(APAPAPGPCPTPAPTPTPAPTPTPAPGPCPTPT)-3') (nucleic acid) DNA (5'-D(TPAPAPGPCPTPAPAPTPAPAPTPAPGPCPTPT)-3') (nucleic acid)
Unique Ligands	BXL

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3MWH	Download File View File

The 1.4 Ang crystal structure of the ArsD arsenic metallochaperone provides insights into its interactions with the ArsA ATPase

Ye, J., Ajees, A.A., Yang, J., Rosen, B.P.

(2010) Biochemistry 49: 5206-5212

Released	2010-05-26
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Escherichia coli
Macromolecule	Arsenical resistance operon trans-acting repressor arsD (protein)
Unique Ligands	GOL

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3N71	Download File View File

Crystal structure of cardiac specific histone methyltransferase SmyD1

Sirinupong, N., Yang, Z.

(2010) J Biol Chem 285: 40635-40644

Released	2010-10-13
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Mus musculus
Macromolecule	Histone lysine methyltransferase SmyD1 (protein)
Unique Ligands	GOL, MES, SFG, ZN

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3P57	Download File View File

Crystal structure of the p300 TAZ2 domain bound to MEF2 on DNA

He, J., Ye, J., Riquelme, C., Liu, J.O.

(2011) Nucleic Acids Res 39: 4464-4474

Released	2011-08-10
Method	X-RAY DIFFRACTION 2.1921 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Histone acetyltransferase p300 (protein) Myocyte-specific enhancer factor 2A (protein) DNA (5'-D(AAPAPCPTPAPTPTPTPAPTPAPAPGPA)-3') (nucleic acid) DNA (5'-D(TPTPCPTPTPAPTPAPAPAPTPAPGPTPT)-3') (nucleic acid)
Unique Ligands	ZN

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3PCU	Download File View File

Crystal structure of human retinoic X receptor alpha ligand-binding domain complexed with LX0278 and SRC1 peptide

Zhang, H., Zhang, Y., Shen, H., Chen, J., Li, C., Chen, L., Hu, L., Jiang, H., Shen, X.

(2012) PLoS One 7: e31811-e31811

Released	2011-11-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Nuclear receptor coactivator 2 (protein) Retinoic acid receptor RXR-alpha (protein)
Unique Ligands	LX8

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4KSM	Download File View File

Crystal structure of Escherichia coli glutraredoxin 2 C9S/C12S mutant without glutathione

Ye, J., Venkadesh, S., Rosen, B.P.

To be published

Released	2014-05-21
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli K-12
Macromolecule	Glutaredoxin-2 (protein)
Unique Ligands	TRS

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4KX4	Download File View File

Crystal structure of Escherichia coli glutaredoxin 2 complex with glutathione

Ye, J., Venkadesh, S., Rosen, B.P.

To be published

Released	2014-05-28
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Escherichia coli K-12
Macromolecule	Glutaredoxin-2 (protein)
Unique Ligands	ACY, GSH

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5DH3	Download File View File

Crystal structure of MST2 in complex with XMU-MP-1

Kong, L.L., Yun, C.H.

(2016) Sci Transl Med 8: 352ra108-352ra108

Released	2016-08-31
Method	X-RAY DIFFRACTION 2.468 Å
Organisms	Homo sapiens
Macromolecule	Serine/threonine-protein kinase 3 (protein)
Unique Ligands	5BS, CL, SO4

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5VTA	Download File View File

Co-Crystal Structure of DPPIV with a Chemibody Inhibitor

Wang, Z., Johnstone, S., Cheng, A.

(2018) Sci Rep 8: 7570-7570

Released	2018-05-09
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mus musculus Rattus norvegicus
Macromolecule	Dipeptidyl peptidase 4 (protein) Fab heavy chain (protein) Fab light chain (protein)
Unique Ligands	9K4, EDO, NAG, PEG, PG4

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6JWP	Download File View File

crystal structure of EGOC

Zhang, T., Ding, J.

(2019) Sci Adv 5: eaax8164-eaax8164

Released	2019-12-11
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Ego2 (protein) GTP-binding protein GTR1 (protein) GTP-binding protein GTR2 (protein) Protein MEH1 (protein) Protein SLM4 (protein)
Unique Ligands	GNP, MG

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6KMR	Download File View File

Crystal structure of human N6amt1-Trm112 in complex with SAM (space group P6122)

Li, W.J., Shi, Y., Zhang, T.L., Ye, J., Ding, J.P.

(2019) Cell Discov 5: 51-51

Released	2019-09-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Methyltransferase N6AMT1 (protein) Multifunctional methyltransferase subunit TRM112-like protein (protein)
Unique Ligands	EDO, SAM

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6KMS	Download File View File

Crystal structure of human N6amt1-Trm112 in complex with SAM (space group I422)

Li, W.J., Shi, Y., Zhang, T.L., Ye, J., Ding, J.P.

(2019) Cell Discov 5: 51-51

Released	2019-09-18
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens
Macromolecule	Methyltransferase N6AMT1 (protein) Multifunctional methyltransferase subunit TRM112-like protein (protein)
Unique Ligands	SAM

1 to 25 of 75 Structures

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