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234,136 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 76 Structures.

Refinements

Structure Determination Methodology

experimental (76)

Scientific Name of Source Organism

	Homo sapiens (44)
	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 (54)
	Bacteria (21)
	Archaea (1)
	Duplodnaviria (1)
	Riboviria (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (49)
	ELECTRON MICROSCOPY (24)
	SOLUTION NMR (3)

Polymer Entity Type

	Protein (76)
	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 (13)
	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)
	2025 - 2029 (1)

Enzyme Classification Name

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

Membrane Protein Annotation

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

Symmetry Type

	Asymmetric (54)
	Cyclic (20)
	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 76 Structures

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1G2S \| pdb_00001g2s	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 \| pdb_00001g2t	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 \| pdb_00001htv	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 \| pdb_00001tlw	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 \| pdb_00001tly	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 \| pdb_00001tlz	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 \| pdb_00001u2w	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 \| pdb_00002n4x	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 \| pdb_00002ppt	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 \| pdb_00002q62	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 \| pdb_00003ivk	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 \| pdb_00003kgk	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 \| pdb_00003kov	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 Biology 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 \| pdb_00003mu6	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 \| pdb_00003mwh	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 \| pdb_00003n71	Download File View File

Crystal structure of cardiac specific histone methyltransferase SmyD1

Sirinupong, N., Yang, Z.

(2010) J Biological 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 \| pdb_00003p57	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 \| pdb_00003pcu	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 \| pdb_00004ksm	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 \| pdb_00004kx4	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 \| pdb_00005dh3	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 \| pdb_00005vta	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 \| pdb_00006jwp	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 \| pdb_00006kmr	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 \| pdb_00006kms	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 76 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

1G2S | pdb_00001g2s

1G2T | pdb_00001g2t

1HTV | pdb_00001htv

1TLW | pdb_00001tlw

1TLY | pdb_00001tly

1TLZ | pdb_00001tlz

1U2W | pdb_00001u2w

2N4X | pdb_00002n4x

2PPT | pdb_00002ppt

2Q62 | pdb_00002q62

3IVK | pdb_00003ivk

3KGK | pdb_00003kgk

3KOV | pdb_00003kov

3MU6 | pdb_00003mu6

3MWH | pdb_00003mwh

3N71 | pdb_00003n71

3P57 | pdb_00003p57

3PCU | pdb_00003pcu

4KSM | pdb_00004ksm

4KX4 | pdb_00004kx4

5DH3 | pdb_00005dh3

5VTA | pdb_00005vta

6JWP | pdb_00006jwp

6KMR | pdb_00006kmr

6KMS | pdb_00006kms