RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Structure Author = "Xing, L."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 22 Structures.

Refinements

Structure Determination Methodology

experimental (22)

Scientific Name of Source Organism

	Severe acute respiratory syndrome coronavirus 2 (13)
	Homo sapiens (12)
	Gammapolyomavirus avis (1)
	Hepatitis E virus (strain Myanmar) (1)
	Paslahepevirus balayani (1)

Taxonomy

	Riboviria (15)
	Eukaryota (12)
	Monodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (12)
	ELECTRON MICROSCOPY (10)

Polymer Entity Type

Protein (22)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (8)
	2.0 - 2.5 (2)
	2.5 - 3.0 (1)
	3.0 - 3.5 (6)
	3.5 - 4.0 (2)
	> 4.5 (2)

Release Date

	2005 - 2009 (4)
	2010 - 2014 (5)
	2020 - 2024 (5)
	2025 - 2029 (8)

Enzyme Classification Name

	Hydrolases (11)
	Transferases (6)

Symmetry Type

	Cyclic (10)
	Asymmetric (10)
	Icosahedral (3)

SCOP Classification

	All beta proteins (5)
	Alpha and beta proteins (a+b) (6)
	All alpha proteins (1)

AllSelected

1 to 22 of 22 Structures

Page 1 of 1

Sort by

Explore in 3D

2ZZQ \| pdb_00002zzq	Download File View File

Crystal structure analysis of the HEV capsid protein, PORF2

Miyazaki, N., Xing, L., Wang, C.-Y., Li, T.-C., Takeda, N., Higashiura, A., Nakagawa, A., Tsukihara, T., Miyamura, T., Cheng, R.H.

To be published

Released	2010-03-09
Method	X-RAY DIFFRACTION 3.81 Å
Organisms	Hepatitis E virus (strain Myanmar)
Macromolecule	Protein ORF3, Capsid protein (protein)

Explore in 3D

3EZR \| pdb_00003ezr	Download File View File

CDK-2 with indazole inhibitor 17 bound at its active site

Kiefer, J.R., Day, J.E., Caspers, N.L., Mathis, K.J., Kretzmer, K.K., Weinberg, R.A., Reitz, B.A., Stegeman, R.A., Trujillo, J.I., Huang, W., Thorarensen, A., Xing, L., Wrightstone, A., Christine, L., Compton, R., Li, X.

(2009) Bioorg Med Chem Lett 19: 908-911

Released	2009-02-03
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Cell division protein kinase 2 (protein)
Unique Ligands	EZR

Explore in 3D

3EZV \| pdb_00003ezv	Download File View File

CDK-2 with indazole inhibitor 9 bound at its active site

(2009) Bioorg Med Chem Lett 19: 908-911

Released	2009-02-03
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Homo sapiens
Macromolecule	Cell division protein kinase 2 (protein)
Unique Ligands	EZV

Explore in 3D

3F5X \| pdb_00003f5x	Download File View File

CDK-2-Cyclin complex with indazole inhibitor 9 bound at its active site

(2009) Bioorg Med Chem Lett 19: 908-911

Released	2009-02-03
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Cell division protein kinase 2 (protein) Cyclin-A2 (protein)
Unique Ligands	EZV, GOL, SO4

Explore in 3D

3IYO \| pdb_00003iyo	Download File View File

Cryo-EM model of virion-sized HEV virion-sized capsid

Xing, L., Mayazaki, N., Li, T.C., Simons, M.N., Wall, J.S., Moore, M., Wang, C.Y., Takeda, N., Wakita, T., Miyamura, T., Cheng, R.H.

(2010) J Biological Chem

Released	2010-08-18
Method	ELECTRON MICROSCOPY 10.5 Å
Organisms	Paslahepevirus balayani
Macromolecule	Capsid protein (protein)

Explore in 3D

3IYS \| pdb_00003iys	Download File View File

Homology model of avian polyomavirus asymmetric unit

Shen, P.S., Enderlein, D., Nelson, C.D.S., Carter, W.S., Kawano, M., Xing, L., Swenson, R.D., Olson, N.H., Baker, T.S., Cheng, R.H., Atwood, W.J., Johne, R., Belnap, D.M.

(2011) Virology 411: 142-152

Released	2011-01-26
Method	ELECTRON MICROSCOPY 11.3 Å
Organisms	Gammapolyomavirus avis
Macromolecule	Major capsid protein VP1 (protein)

Explore in 3D

3KF7 \| pdb_00003kf7	Download File View File

Crystal Structure of Human p38alpha Complexed With a Triazolopyrimidine compound

Shieh, H.-S., Williams, J.M., Stegeman, R.A., Xing, L., Jerome, K.D.

(2010) Bioorg Med Chem Lett 20: 469-473

Released	2009-12-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Mitogen-activated protein kinase 14 (protein)
Unique Ligands	L9G

Explore in 3D

3ROC \| pdb_00003roc	Download File View File

Crystal structure of human p38 alpha complexed with a pyrimidinone compound

Shieh, H.-S., Xing, L.

(2011) Bioorg Med Chem Lett 21: 3856-3860

Released	2011-06-15
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Mitogen-activated protein kinase 14 (protein)
Unique Ligands	29A, 29B

Explore in 3D

4HCT \| pdb_00004hct	Download File View File

Crystal structure of ITK in complex with compound 52

Zapf, C.W., Gerstenberger, B.S., Xing, L., Limburg, D.C., Anderson, D.R., Caspers, N., Han, S., Aulabaugh, A., Kurumbail, R., Shakya, S., Li, X., Spaulding, V., Czerwinski, R.M., Seth, N., Medley, Q.G.

(2012) J Med Chem 55: 10047-10063

Released	2012-11-14
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase ITK/TSK (protein)
Unique Ligands	18R

Explore in 3D

7JST \| pdb_00007jst	Download File View File

Crystal structure of SARS-CoV-2 3CL in apo form

Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.-Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.

(2021) Nat Commun 12: 2016-2016

Released	2021-03-03
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	3C-like proteinase (protein)
Unique Ligands	PO4

Explore in 3D

7JSU \| pdb_00007jsu	Download File View File

Crystal structure of SARS-CoV-2 3CL protease in complex with GC376

Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.-Y., Nair, M.S., Zask, A., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.

(2021) Nat Commun 12: 2016-2016

Released	2021-03-10
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	3C-like proteinase (protein)
Unique Ligands	PO4, UED

Explore in 3D

7JT0 \| pdb_00007jt0	Download File View File

Crystal structure of SARS-CoV-2 3CL protease in complex with MAC5576

Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.-Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.

(2021) Nat Commun 12: 2016-2016

Released	2021-03-10
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	3C-like proteinase (protein)
Unique Ligands	LW1, PO4

Explore in 3D

7JT7 \| pdb_00007jt7	Download File View File

Crystal structure of SARS-CoV-2 3CL protease in complex with compound 4

Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.-Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.

(2021) Nat Commun 12: 2016-2016

Released	2021-03-17
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	3C-like proteinase (protein)
Unique Ligands	TG3

Explore in 3D

7JW8 \| pdb_00007jw8	Download File View File

Crystal structure of SARS-CoV-2 3CL protease in complex with compound 4 in space group P1

Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.-Y., Nair, M.S., Zask, A., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.

(2021) Nat Commun 12: 2016-2016

Released	2021-03-10
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	3C-like proteinase (protein)
Unique Ligands	BTB, TG3

Explore in 3D

8Z3W \| pdb_00008z3w	Download File View File

Cryo-EM structure of SARS-CoV-2 D614G S with one ACE2 receptor binding (RB1) in prefusion conformation

Liu, Z., Xing, L.

To be published

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3.45 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

Explore in 3D

8Z4X \| pdb_00008z4x	Download File View File

Cryo-EM structure of SARS-CoV-2 D614G S with two ACE2 receptors binding (RB2) in prefusion conformation

Liu, Z., Xing, L.

To be published

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, NAG

Explore in 3D

8Z64 \| pdb_00008z64	Download File View File

Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation (focused refinement of NTD-SD1-RBD-ACE2)

Liu, Z., Xing, L.

To be published

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3.53 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

Explore in 3D

8Z6A \| pdb_00008z6a	Download File View File

Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation

Liu, Z., Xing, L.

To be published

Released	2025-02-05
Method	ELECTRON MICROSCOPY 2.99 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, NAG

Explore in 3D

8Z7B \| pdb_00008z7b	Download File View File

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-ACE2)

Liu, Z., Xing, L.

To be published

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, NAG

Explore in 3D

8Z7G \| pdb_00008z7g	Download File View File

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of intact S2)

Liu, Z., Xing, L.

To be published

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3.06 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG

Explore in 3D

8Z7L \| pdb_00008z7l	Download File View File

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of S-bottom)

Liu, Z., Xing, L.

To be published

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3.42 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

Explore in 3D

8Z7P \| pdb_00008z7p	Download File View File

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC)

Liu, Z., Xing, L.

To be published

Released	2025-02-05
Method	ELECTRON MICROSCOPY 3.45 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, NAG

1 to 22 of 22 Structures

Page 1 of 1

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

2ZZQ | pdb_00002zzq

3EZR | pdb_00003ezr

3EZV | pdb_00003ezv

3F5X | pdb_00003f5x

3IYO | pdb_00003iyo

3IYS | pdb_00003iys

3KF7 | pdb_00003kf7

3ROC | pdb_00003roc

4HCT | pdb_00004hct

7JST | pdb_00007jst

7JSU | pdb_00007jsu

7JT0 | pdb_00007jt0

7JT7 | pdb_00007jt7

7JW8 | pdb_00007jw8

8Z3W | pdb_00008z3w

8Z4X | pdb_00008z4x

8Z64 | pdb_00008z64

8Z6A | pdb_00008z6a

8Z7B | pdb_00008z7b

8Z7G | pdb_00008z7g

8Z7L | pdb_00008z7l

8Z7P | pdb_00008z7p