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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Xiong, R."

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Search Summary

This query matches 32 Structures.

Refinements

Structure Determination Methodology

experimental (32)

Scientific Name of Source Organism

	Homo sapiens (19)
	Saccharomyces cerevisiae (5)
	Severe acute respiratory syndrome coronavirus 2 (5)
	Arabidopsis thaliana (2)
	Escherichia coli (1)

Taxonomy

	Eukaryota (26)
	Riboviria (5)
	Bacteria (1)

Experimental Method

X-RAY DIFFRACTION (32)

Polymer Entity Type

Protein (32)

Refinement Resolution (Å)

	1.0 - 1.5 (8)
	1.5 - 2.0 (4)
	2.0 - 2.5 (12)
	2.5 - 3.0 (7)
	3.0 - 3.5 (1)

Release Date

	2010 - 2014 (5)
	2015 - 2019 (3)
	2020 - 2024 (24)

Enzyme Classification Name

	Transferases (9)
	Hydrolases (7)
	Lyases (1)
	Oxidoreductases (1)

Membrane Protein Annotation

OPM (2)

Symmetry Type

	Asymmetric (18)
	Cyclic (13)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (11)
	Artifacts (5)
	All alpha proteins (1)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 25 of 32 Structures

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4AS9 \| pdb_00004as9	Download File View File

The structure of modified benzoquinone ansamycins bound to yeast N- terminal Hsp90

Roe, S.M., Prodromou, C.

(2013) Nat Chem 5: 307-314

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.71 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 (protein)
Unique Ligands	4QS

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4ASA \| pdb_00004asa	Download File View File

The structure of modified benzoquinone ansamycins bound to yeast N- terminal Hsp90

Roe, S.M., Prodromou, C.

(2013) Nat Chem 5: 307

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 (protein)
Unique Ligands	59C, CL

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4ASB \| pdb_00004asb	Download File View File

The structure of modified benzoquinone ansamycins bound to yeast N- terminal Hsp90

Roe, S.M., Prodromou, C.

(2013) Nat Chem 5: 307-314

Released	2013-04-03
Method	X-RAY DIFFRACTION 3.08 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 (protein)
Unique Ligands	8TO

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4ASF \| pdb_00004asf	Download File View File

The structure of modified benzoquinone ansamycins bound to yeast N- terminal Hsp90

Roe, S.M., Prodromou, C.

(2013) Nat Chem 5: 307-314

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 (protein)
Unique Ligands	62U, NI

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4ASG \| pdb_00004asg	Download File View File

The structure of modified benzoquinone ansamycins bound to yeast N- terminal Hsp90

Roe, S.M., Prodromou, C.

(2013) Nat Chem 5: 307

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 (protein)
Unique Ligands	814, NI

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5GIT \| pdb_00005git	Download File View File

BTB domain of KEAP1 in complex with XX3

Zhu, L.L., Li, H.L., Wu, F.S., Xiong, R.

(2017) Antioxid Redox Signal 27: 754-768

Released	2017-06-28
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Homo sapiens
Macromolecule	Kelch-like ECH-associated protein 1 (protein)
Unique Ligands	XXT

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6KZ8 \| pdb_00006kz8	Download File View File

Crystal structure of plant Phospholipase D alpha complex with phosphatidic acid

Li, J.X., Yu, F., Zhang, P.

(2020) Cell Res 30: 61-69

Released	2019-11-13
Method	X-RAY DIFFRACTION 2.291 Å
Organisms	Arabidopsis thaliana
Macromolecule	Phospholipase D alpha 1 (protein)
Unique Ligands	CA, PA8

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6KZ9 \| pdb_00006kz9	Download File View File

Crystal structure of plant Phospholipase D alpha

Li, J.X., Yu, F., Zhang, P.

(2020) Cell Res 30: 61-69

Released	2019-10-30
Method	X-RAY DIFFRACTION 1.801 Å
Organisms	Arabidopsis thaliana
Macromolecule	Phospholipase D alpha 1 (protein)
Unique Ligands	CA

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6M2B \| pdb_00006m2b	Download File View File

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with S416

Zhu, L., Li, H.

(2020) Protein Cell 11: 723-739

Released	2021-03-03
Method	X-RAY DIFFRACTION 1.76 Å
Organisms	Homo sapiens
Macromolecule	Dihydroorotate dehydrogenase (quinone), mitochondrial (protein)
Unique Ligands	EZO, FMN, ORO

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6P05 \| pdb_00006p05	Download File View File

Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with compound 27

Ratia, K.M., Xiong, R., Li, Y., Zhao, J., Gutgesell, L.M., Shen, Z., Dye, K., Dubrovyskyii, O., Zhao, H., Huang, F., Tonetti, D.A., Thatcher, G.R.

(2020) J Med Chem 63: 7186-7210

Released	2020-05-20
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Homo sapiens
Macromolecule	Bromodomain-containing protein 4 (protein)
Unique Ligands	GOL, YF2

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7JHD \| pdb_00007jhd	Download File View File

Estrogen Receptor Alpha Ligand Binding Domain Y537S in Complex with TTC-352 and GRIP Peptide

Fanning, S.W., Abderraman, B., Maximov, P.Y., Jordan, V.C., Greene, G.L.

(2021) Mol Cancer Ther 20: 11-25

Released	2020-11-25
Method	X-RAY DIFFRACTION 2.402 Å
Organisms	Homo sapiens
Macromolecule	Estrogen receptor (protein) Nuclear receptor coactivator 2 (protein)
Unique Ligands	V9J

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7JKW \| pdb_00007jkw	Download File View File

Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with ZN1-99

Ratia, K.M., Xiong, R., Li, Y., Shen, Z., Zhao, J., Huang, F., Dubrovyskyii, O., Thatcher, G.R.

(2020) J Med Chem 63: 7186-7210

Released	2021-08-25
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Homo sapiens
Macromolecule	Bromodomain-containing protein 4 (protein)
Unique Ligands	VCV

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7JKX \| pdb_00007jkx	Download File View File

Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with YF3-6

Ratia, K.M., Xiong, R., Li, Y., Shen, Z., Zhao, J., Huang, F., Dubrovyskyii, O., Thatcher, G.R.

To be published

Released	2021-06-23
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Homo sapiens
Macromolecule	Bromodomain-containing protein 4 (protein)
Unique Ligands	Y36

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7JKY \| pdb_00007jky	Download File View File

Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with YF3-126

Ratia, K.M., Xiong, R., Li, Y., Shen, Z., Zhao, J., Huang, F., Dubrovyskyii, O., Thatcher, G.R.

(2020) J Med Chem 63: 7186-7210

Released	2021-08-25
Method	X-RAY DIFFRACTION 1.16 Å
Organisms	Homo sapiens
Macromolecule	Bromodomain-containing protein 4 (protein)
Unique Ligands	NA, YF6

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7JKZ \| pdb_00007jkz	Download File View File

Bromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) complexed with YF3-126

Ratia, K.M., Xiong, R., Li, Y., Shen, Z., Zhao, J., Huang, F., Dubrovyskyii, O., Thatcher, G.R.

(2020) J Med Chem 63: 7186-7210

Released	2021-08-25
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Homo sapiens
Macromolecule	Bromodomain-containing protein 4 (protein)
Unique Ligands	EDO, GOL, YF6

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7JUO \| pdb_00007juo	Download File View File

CBP bromodomain complexed with YF2-23

Ratia, K.M., Xiong, R., Principe, D., Li, Y., Huang, F., Rana, A., Thatcher, G.

(2022) Proc Natl Acad Sci U S A 119:

Released	2021-09-01
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	CREB-binding protein (protein)
Unique Ligands	YF2

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7LBR \| pdb_00007lbr	Download File View File

SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-89

Ratia, K.M., Xiong, R., Thatcher, G.R.

(2021) bioRxiv

Released	2021-02-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Non-structural protein 3 (protein)
Unique Ligands	GOL, SO4, XT7, ZN

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7LBS \| pdb_00007lbs	Download File View File

SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-24

Ratia, K.M., Xiong, R., Thatcher, G.R.

(2021) bioRxiv

Released	2021-02-24
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Non-structural protein 3 (protein)
Unique Ligands	BO3, GOL, SO4, XR8, ZN

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7LLF \| pdb_00007llf	Download File View File

SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-83

Ratia, K.M., Xiong, R., Thatcher, G.R.

(2021) bioRxiv

Released	2021-02-24
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Non-structural protein 3 (protein)
Unique Ligands	BO3, GOL, SO4, Y54, ZN

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7LLZ \| pdb_00007llz	Download File View File

SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-69

Ratia, K.M., Xiong, R., Thatcher, G.R.

(2021) bioRxiv

Released	2021-02-24
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Non-structural protein 3 (protein)
Unique Ligands	SO4, Y61, ZN

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7LOS \| pdb_00007los	Download File View File

SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-65

Ratia, K.M., Xiong, R., Thatcher, G.R.

(2021) bioRxiv

Released	2021-02-24
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Non-structural protein 3 (protein)
Unique Ligands	CL, SO4, Y97, ZN

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7QXF \| pdb_00007qxf	Download File View File

Fructose-6-phosphate aldolase (FSA) mutant R134V, S166G, with covalently bound active site ligand

Dobritzsch, D., Widersten, M., Engel, S.

(2023) Catal Sci Technol 13: 4978-4987

Released	2023-02-08
Method	X-RAY DIFFRACTION 2.62 Å
Organisms	Escherichia coli
Macromolecule	Fructose-6-phosphate aldolase 1 (protein)

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7RUH \| pdb_00007ruh	Download File View File

Bromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) complexed with XR844

Ratia, K.M., Xiong, R., Li, Y., Shen, Z., Zhao, J., Huang, F., Dubrovyskyii, O., Thatcher, G.R.

To be published

Released	2022-08-24
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Bromodomain-containing protein 4 (protein)
Unique Ligands	7QZ

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7RUI \| pdb_00007rui	Download File View File

Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with XR844

Ratia, K.M., Xiong, R., Li, Y., Shen, Z., Zhao, J., Huang, F., Dubrovyskyii, O., Thatcher, G.R.

To be published

Released	2022-08-24
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Homo sapiens
Macromolecule	Bromodomain-containing protein 4 (protein)
Unique Ligands	7QZ

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8DSC \| pdb_00008dsc	Download File View File

Human NAMPT in complex with substrate NAM and small molecule activator NP-A1-R

Ratia, K., Xiong, R., Shen, Z., Thatcher, G.R.

(2023) Biochemistry 62: 923-933

Released	2023-03-08
Method	X-RAY DIFFRACTION 1.321 Å
Organisms	Homo sapiens
Macromolecule	Nicotinamide phosphoribosyltransferase (protein)
Unique Ligands	CL, GOL, NA, NCA, PO4, TIE

1 to 25 of 32 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

4AS9 | pdb_00004as9

4ASA | pdb_00004asa

4ASB | pdb_00004asb

4ASF | pdb_00004asf

4ASG | pdb_00004asg

5GIT | pdb_00005git

6KZ8 | pdb_00006kz8

6KZ9 | pdb_00006kz9

6M2B | pdb_00006m2b

6P05 | pdb_00006p05

7JHD | pdb_00007jhd

7JKW | pdb_00007jkw

7JKX | pdb_00007jkx

7JKY | pdb_00007jky

7JKZ | pdb_00007jkz

7JUO | pdb_00007juo

7LBR | pdb_00007lbr

7LBS | pdb_00007lbs

7LLF | pdb_00007llf

7LLZ | pdb_00007llz

7LOS | pdb_00007los

7QXF | pdb_00007qxf

7RUH | pdb_00007ruh

7RUI | pdb_00007rui

8DSC | pdb_00008dsc