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: Citation Author = "Cai, Y."

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 186 Structures.

Refinements

Structure Determination Methodology

experimental (186)

Scientific Name of Source Organism

	Homo sapiens (55)
	Severe acute respiratory syndrome coronavirus 2 (31)
	Ebinur lake virus (15)
	Human immunodeficiency virus 1 (12)
	synthetic construct (10)
	Hepatitis B virus (7)
	Mus musculus (6)
	Aspergillus flavus NRRL3357 (5)
	Enterovirus A71 (5)
	Siraitia grosvenorii (5)

More...

Taxonomy

	Eukaryota (96)
	Riboviria (73)
	Bacteria (20)
	other sequences (10)
	Duplodnaviria (2)

Experimental Method

	X-RAY DIFFRACTION (111)
	ELECTRON MICROSCOPY (68)
	SOLUTION NMR (7)

Polymer Entity Type

	Protein (183)
	DNA (7)
	RNA (7)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (4)
	1.5 - 2.0 (40)
	2.0 - 2.5 (43)
	2.5 - 3.0 (27)
	3.0 - 3.5 (34)
	3.5 - 4.0 (18)
	4.0 - 4.5 (9)
	> 4.5 (3)

Release Date

	2000 - 2004 (9)
	2005 - 2009 (2)
	2010 - 2014 (22)
	2015 - 2019 (36)
	2020 - 2024 (112)
	2025 - 2029 (5)

Enzyme Classification Name

	Transferases (62)
	Hydrolases (40)
	Oxidoreductases (5)
	Lyases (4)

Membrane Protein Annotation

	OPM (9)
	PDBTM (6)
	mpstruc (5)
	MemProtMD (5)

Symmetry Type

	Asymmetric (110)
	Cyclic (66)
	Icosahedral (10)
	Dihedral (6)
	Helical (1)

SCOP Classification

	Alpha and beta proteins (a/b) (22)
	All beta proteins (19)
	All alpha proteins (6)
	Artifacts (7)
	Alpha and beta proteins (a+b) (3)

AllSelected

1 to 25 of 186 Structures

Page 1 of 8

Sort by

Explore in 3D

1Q6X \| pdb_00001q6x	Download File View File

Crystal structure of rat choline acetyltransferase

Cai, Y., Rodgers, D.W.

(2004) EMBO J 23: 2047-2058

Released	2004-06-01
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Rattus norvegicus
Macromolecule	choline O-acetyltransferase (protein)
Unique Ligands	NA

Explore in 3D

1R7T \| pdb_00001r7t	Download File View File

Glycosyltransferase A in complex with 3-deoxy-acceptor analog inhibitor

Nguyen, H.P., Seto, N.O.L., Cai, Y., Leinala, E.K., Borisova, S.N., Palcic, M.M., Evans, S.V.

(2003) J Biological Chem 278: 49191-49195

Released	2004-02-10
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Homo sapiens
Macromolecule	Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase (protein)
Unique Ligands	HG
Unique branched monosaccharides	DLG, FUC

Explore in 3D

1R7U \| pdb_00001r7u	Download File View File

Glycosyltransferase B in complex with 3-deoxy-acceptor analog inhibitor

Nguyen, H.P., Seto, N.O.L., Cai, Y., Leinala, E.K., Borisova, S.N., Palcic, M.M., Evans, S.V.

(2003) J Biological Chem 278: 49191-49195

Released	2004-02-10
Method	X-RAY DIFFRACTION 1.61 Å
Organisms	Homo sapiens
Macromolecule	Glycoprotein-fucosylgalactoside alpha-galactosyltransferase (protein)
Unique Ligands	HG
Unique branched monosaccharides	DLG, FUC

Explore in 3D

1R7V \| pdb_00001r7v	Download File View File

Glycosyltransferase A in complex with 3-amino-acceptor analog inhibitor

Nguyen, H.P., Seto, N.O.L., Cai, Y., Leinala, E.K., Borisova, S.N., Palcic, M.M., Evans, S.V.

(2003) J Biological Chem 278: 49191-49195

Released	2004-02-10
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Homo sapiens
Macromolecule	Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase (protein)
Unique Ligands	HG
Unique branched monosaccharides	AIG, FUC

Explore in 3D

1R7X \| pdb_00001r7x	Download File View File

Glycosyltransferase B in complex with 3-amino-acceptor analog inhibitor

Nguyen, H.P., Seto, N.O.L., Cai, Y., Leinala, E.K., Borisova, S.N., Palcic, M.M., Evans, S.V.

(2003) J Biological Chem 278: 49191-49195

Released	2004-02-10
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Homo sapiens
Macromolecule	Glycoprotein-fucosylgalactoside alpha-galactosyltransferase (protein)
Unique Ligands	HG
Unique branched monosaccharides	AIG, FUC

Explore in 3D

1R7Y \| pdb_00001r7y	Download File View File

Glycosyltransferase A in complex with 3-amino-acceptor analog inhibitor and uridine diphosphate

Nguyen, H.P., Seto, N.O.L., Cai, Y., Leinala, E.K., Borisova, S.N., Palcic, M.M., Evans, S.V.

(2003) J Biological Chem 278: 49191-49195

Released	2004-02-10
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase (protein)
Unique Ligands	HG, MN, UDP
Unique branched monosaccharides	AIG, FUC

Explore in 3D

1R80 \| pdb_00001r80	Download File View File

Glycosyltransferase B in complex with 3-amino-acceptor analog inhibitor and uridine diphosphate

Nguyen, H.P., Seto, N.O.L., Cai, Y., Leinala, E.K., Borisova, S.N., Palcic, M.M., Evans, S.V.

(2003) J Biological Chem 278: 49191-49195

Released	2004-02-10
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Glycoprotein-fucosylgalactoside alpha-galactosyltransferase (protein)
Unique Ligands	HG, MN, UDP
Unique branched monosaccharides	AIG, FUC

Explore in 3D

1R81 \| pdb_00001r81	Download File View File

Glycosyltransferase A in complex with 3-amino-acceptor analog inhibitor and uridine diphosphate-N-acetyl-galactose

Nguyen, H.P., Seto, N.O.L., Cai, Y., Leinala, E.K., Borisova, S.N., Palcic, M.M., Evans, S.V.

(2003) J Biological Chem 278: 49191-49195

Released	2004-02-10
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase (protein)
Unique Ligands	HG, UD2
Unique branched monosaccharides	AIG, FUC

Explore in 3D

1R82 \| pdb_00001r82	Download File View File

Glycosyltransferase B in complex with 3-amino-acceptor analog inhibitor, and uridine diphosphate-galactose

Nguyen, H.P., Seto, N.O.L., Cai, Y., Leinala, E.K., Borisova, S.N., Palcic, M.M., Evans, S.V.

(2003) J Biological Chem 278: 49191-49195

Released	2004-02-10
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Glycoprotein-fucosylgalactoside alpha-galactosyltransferase (protein)
Unique Ligands	GDU, HG
Unique branched monosaccharides	AOG, FUC

Explore in 3D

2LZK \| pdb_00002lzk	Download File View File

NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing

Tang, Y., Liu, Z., Ding, S., Lin, C.H., Cai, Y., Rodriguez, F.A., Sayer, J.M., Jerina, D.M., Amin, S., Broyde, S., Geacintov, N.E.

(2012) Biochemistry 51: 9751-9762

Released	2012-11-21
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(CPCPAPTPCPGPCPTPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPAPGPCPGPAPTPGPG)-3') (nucleic acid)
Unique Ligands	14L

Explore in 3D

2MIV \| pdb_00002miv	Download File View File

NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations

Rodriguez, F.A., Liu, Z., Lin, C.H., Ding, S., Cai, Y., Kolbanovskiy, A., Kolbanovskiy, M., Amin, S., Broyde, S., Geacintov, N.E.

(2014) Biochemistry 53: 1827-1841

Released	2014-04-02
Method	SOLUTION NMR
Macromolecule	DNA_(5'-D(CPCPAPTPCPGPCPTPAPCPC)-3') (nucleic acid) DNA_(5'-D(GPGPTPAPGPGPAPTPGP*G)-3') (nucleic acid)
Unique Ligands	2QL

Explore in 3D

2MIW \| pdb_00002miw	Download File View File

Nuclear magnetic resonance studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations

Rodriguez, F.A., Liu, Z., Lin, C.H., Ding, S., Cai, Y., Kolbanovskiy, A., Kolbanovskiy, M., Amin, S., Broyde, S., Geacintov, N.E.

(2014) Biochemistry 53: 1827-1841

Released	2014-04-02
Method	SOLUTION NMR
Macromolecule	DNA_(5'-D(CPCPAPTPCPGPCPTPAPCPC)-3') (nucleic acid) DNA_(5'-D(GPGPTPAPGPCPGPAPTPGPG)-3') (nucleic acid)
Unique Ligands	2QL

Explore in 3D

3CPM \| pdb_00003cpm	Download File View File

plant peptide deformylase PDF1B crystal structure

Rodgers, D.W., Houtz, R.L., Dirk, L.M.A., Schmidt, J.J., Cai, Y.

(2008) Biochem J 413: 417-427

Released	2008-07-22
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Arabidopsis thaliana
Macromolecule	Peptide deformylase, chloroplast (protein)
Unique Ligands	SO4, ZN

Explore in 3D

3CUE \| pdb_00003cue	Download File View File

Crystal structure of a TRAPP subassembly activating the Rab Ypt1p

Cai, Y., Reinisch, K.M.

(2008) Cell 133: 1202-1213

Released	2008-07-08
Method	X-RAY DIFFRACTION 3.7 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	GTP-binding protein YPT1 (protein) Transport protein particle 18 kDa subunit (protein) Transport protein particle 22 kDa subunit (protein) Transport protein particle 23 kDa subunit (protein) Transport protein particle 31 kDa subunit (protein)
Unique Ligands	PLM

Explore in 3D

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

Explore in 3D

3TW8 \| pdb_00003tw8	Download File View File

GEF domain of DENND 1B in complex with Rab GTPase Rab35

Wu, X.D., Kummel, D., Reinisch, K.M.

(2011) Proc Natl Acad Sci U S A 108: 18672-18677

Released	2011-11-16
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	DENN domain-containing protein 1B (protein) Ras-related protein Rab-35 (protein)

Explore in 3D

4DQB \| pdb_00004dqb	Download File View File

Crystal Structure of wild-type HIV-1 Protease in Complex with DRV

Schiffer, C.A., Mittal, S.

(2012) J Am Chem Soc 134: 4163-4168

Released	2012-03-07
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	Aspartyl protease (protein)
Unique Ligands	017, DMS, EDO, PO4

Explore in 3D

4DQC \| pdb_00004dqc	Download File View File

Crystal Structure of (G16C/L38C) HIV-1 Protease in Complex with DRV

Schiffer, C.A., Mittal, S.

(2012) J Am Chem Soc 134: 4163-4168

Released	2012-03-07
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	Aspartyl protease (protein)
Unique Ligands	017, GOL, PO4

Explore in 3D

4DQE \| pdb_00004dqe	Download File View File

Crystal Structure of (G16C/L38C) HIV-1 Protease in Complex with DRV

Schiffer, C.A., Mittal, S.

(2012) J Am Chem Soc 134: 4163-4168

Released	2012-03-07
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	Aspartyl protease (protein)
Unique Ligands	017, ACT

Explore in 3D

4DQF \| pdb_00004dqf	Download File View File

Crystal Structure of (G16A/L38A) HIV-1 Protease in Complex with DRV

Schiffer, C.A., Mittal, S.

(2012) J Am Chem Soc 134: 4163-4168

Released	2012-03-07
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	Aspartyl protease (protein)
Unique Ligands	017, EDO, GOL, SO4

Explore in 3D

4DQG \| pdb_00004dqg	Download File View File

Crystal Structure of apo(G16C/L38C) HIV-1 Protease

Schiffer, C.A., Mittal, S.

(2012) J Am Chem Soc 134: 4163-4168

Released	2012-03-07
Method	X-RAY DIFFRACTION 2.79 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	Aspartyl protease (protein)
Unique Ligands	ACT, GOL, HGU, OXY, PO4

Explore in 3D

4DQH \| pdb_00004dqh	Download File View File

Crystal Structure of (R14C/E65C) HIV-1 Protease in complex with DRV

Schiffer, C.A., Mittal, S.

(2012) J Am Chem Soc 134: 4163-4168

Released	2012-03-07
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	Wild-type HIV-1 protease dimer (protein)
Unique Ligands	017, GOL

Explore in 3D

4FVB \| pdb_00004fvb	Download File View File

Crystal structure of EV71 2A proteinase C110A mutant

Cai, Q., Muhammad, Y., Liu, W., Gao, Z., Peng, X., Cai, Y., Wu, C., Zheng, Q., Li, J., Lin, T.

(2013) J Virol 87: 7348-7356

Released	2013-06-19
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Enterovirus A71
Macromolecule	2A proteinase (protein)
Unique Ligands	ZN

Explore in 3D

4FVD \| pdb_00004fvd	Download File View File

Crystal structure of EV71 2A proteinase C110A mutant in complex with substrate

Cai, Q., Muhammad, Y., Liu, W., Gao, Z., Peng, X., Cai, Y., Wu, C., Zheng, Q., Li, J., Lin, T.

(2013) J Virol 87: 7348-7356

Released	2013-06-19
Method	X-RAY DIFFRACTION 1.66 Å
Organisms	Enterovirus A71
Macromolecule	10-mer peptide from 2A proteinase (protein) 2A proteinase (protein)
Unique Ligands	ZN

Explore in 3D

4GH6 \| pdb_00004gh6	Download File View File

Crystal structure of the PDE9A catalytic domain in complex with inhibitor 28

Hou, J., Ke, H.

(2012) J Med Chem 55: 8549-8558

Released	2012-10-03
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A (protein)
Unique Ligands	LUO, MG, ZN

1 to 25 of 186 Structures

Page 1 of 8

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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1Q6X | pdb_00001q6x

1R7T | pdb_00001r7t

1R7U | pdb_00001r7u

1R7V | pdb_00001r7v

1R7X | pdb_00001r7x

1R7Y | pdb_00001r7y

1R80 | pdb_00001r80

1R81 | pdb_00001r81

1R82 | pdb_00001r82

2LZK | pdb_00002lzk

2MIV | pdb_00002miv

2MIW | pdb_00002miw

3CPM | pdb_00003cpm

3CUE | pdb_00003cue

3P57 | pdb_00003p57

3TW8 | pdb_00003tw8

4DQB | pdb_00004dqb

4DQC | pdb_00004dqc

4DQE | pdb_00004dqe

4DQF | pdb_00004dqf

4DQG | pdb_00004dqg

4DQH | pdb_00004dqh

4FVB | pdb_00004fvb

4FVD | pdb_00004fvd

4GH6 | pdb_00004gh6