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

234,785 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 = "Sun, D."

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 35 Structures.

Refinements

Structure Determination Methodology

experimental (35)

Scientific Name of Source Organism

	Homo sapiens (17)
	Escherichia coli K-12 (8)
	synthetic construct (4)
	Drosophila melanogaster (2)
	Saccharomyces cerevisiae (2)
	Alistipes putredinis (1)
	Conus geographus (1)
	Conus marmoreus (1)
	Conus striatus (1)
	Conus tulipa (1)

More...

Taxonomy

	Eukaryota (24)
	Bacteria (10)
	other sequences (4)
	Eukaryota (eukaryotes) (1)

Experimental Method

	X-RAY DIFFRACTION (29)
	ELECTRON MICROSCOPY (5)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (30)
	DNA (22)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (13)
	2.0 - 2.5 (3)
	2.5 - 3.0 (6)
	3.0 - 3.5 (6)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (2)
	2010 - 2014 (13)
	2015 - 2019 (9)
	2020 - 2024 (10)

Enzyme Classification Name

	Oxidoreductases (10)
	Hydrolases (5)

Membrane Protein Annotation

	MemProtMD (3)
	OPM (1)

Symmetry Type

	Asymmetric (24)
	Cyclic (8)
	Dihedral (3)

SCOP Classification

	All beta proteins (8)
	All alpha proteins (2)
	Alpha and beta proteins (a/b) (2)
	Alpha and beta proteins (a+b) (1)
	Small proteins (1)

AllSelected

1 to 25 of 35 Structures

Page 1 of 2

Sort by

Explore in 3D

1FYG \| pdb_00001fyg	Download File View File

Solution structure of omega conotoxin SO3 determined by 1H-NMR

Yan, Y., Zhang, R.

(2003) Chin Sci Bull 48: 1097-1102

Released	2000-10-18
Method	SOLUTION NMR
Organisms	Conus striatus
Macromolecule	OMEGA CONOTOXIN SO3 (protein)

Explore in 3D

2DPQ \| pdb_00002dpq	Download File View File

The crystal structures of the calcium-bound con-G and con-T(K7gamma) dimeric peptides demonstrate a novel metal-dependent helix-forming motif

Cnudde, S.E., Prorok, M., Dai, Q., Castellino, F.J., Geiger, J.H.

(2007) J Am Chem Soc 129: 1586-1593

Released	2007-04-24
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Conus geographus
Macromolecule	Conantokin-G (protein)
Unique Ligands	CA, CL

Explore in 3D

2DPR \| pdb_00002dpr	Download File View File

The crystal structures of the calcium-bound con-G and con-T(K7Glu) dimeric peptides demonstrate a novel metal-dependent helix-forming motif

Cnudde, S.E., Prorok, M., Dai, Q., Castellino, F.J., Geiger, J.H.

(2007) J Am Chem Soc 129: 1586-1593

Released	2007-04-24
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Conus tulipa
Macromolecule	Conantokin-T (protein)
Unique Ligands	CA

Explore in 3D

3O1M \| pdb_00003o1m	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(TAPGPGPTPAPAP(ME6)PAPCPCPGPT)-3') (nucleic acid)
Unique Ligands	AKG, MN

Explore in 3D

3O1O \| pdb_00003o1o	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(TAPGPGPTPAPAP(MFT)PAPCPCPGPT)-3') (nucleic acid)
Unique Ligands	AKG, MN

Explore in 3D

3O1P \| pdb_00003o1p	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.51 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(TAPGPGPTPAPAP(EDA)PAPCPCPGPT)-3') (nucleic acid)
Unique Ligands	AKG, GOL, MN

Explore in 3D

3O1R \| pdb_00003o1r	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(APGPGPTPAPAP(MDK)PAPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	AKG, GOL, MN

Explore in 3D

3O1S \| pdb_00003o1s	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(APGPGPTPAPAP(MDQ)PAPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	FE, SIN

Explore in 3D

3O1T \| pdb_00003o1t	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(APGPGPTPAPAP(MDU)PAPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	FE, SIN

Explore in 3D

3O1U \| pdb_00003o1u	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(APGPGPTPAPAP(MDV)PAPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	FE, SIN

Explore in 3D

3O1V \| pdb_00003o1v	Download File View File

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

(2010) Nature 468: 330-333

Released	2010-11-17
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli K-12
Macromolecule	Alpha-ketoglutarate-dependent dioxygenase AlkB (protein) DNA (5'-D(APAPCPGPGPTPAPTPTPAPCPCPT)-3') (nucleic acid) DNA (5'-D(APGPGPTPAPAP(MDJ)PAPCPCPGP*T)-3') (nucleic acid)
Unique Ligands	FE, SIN

Explore in 3D

3UO7 \| pdb_00003uo7	Download File View File

Crystal structure of Human Thymine DNA Glycosylase Bound to Substrate 5-carboxylcytosine

Zhang, L., He, C.

(2012) Nat Chem Biol 8: 328-330

Released	2012-02-15
Method	X-RAY DIFFRACTION 3.002 Å
Organisms	Homo sapiens
Macromolecule	G/T mismatch-specific thymine DNA glycosylase (protein) 5'-D(CPAPGPCPTPCPTPGPTPAPCPAPTPGPAPGPCPAPGPTPGPGPA)-3' (nucleic acid) 5'-D(CPCPAPCPTPGPCPTPCPAP(1CC)PGPTPAPCPAPGPAPGPCPTPGPT)-3' (nucleic acid)

Explore in 3D

3UOB \| pdb_00003uob	Download File View File

Crystal structure of Human Thymine DNA Glycosylase Bound to Substrate Analog 2'-deoxy-2'-beta-fluoro-cytidine

Zhang, L., He, C.

(2012) Nat Chem Biol 8: 328-330

Released	2012-02-15
Method	X-RAY DIFFRACTION 3.011 Å
Organisms	Homo sapiens
Macromolecule	G/T mismatch-specific thymine DNA glycosylase (protein) 5'-D(CPAPGPCPTPCPTPGPTPAPCPGPTPGPAPGPCPAPGPTPGPGPA)-3' (nucleic acid) 5'-D(CPCPAPCPTPGPCPTPCPAP(1FC)PGPTPAPCPAPGPAPGPCPTPGPT)-3' (nucleic acid)

Explore in 3D

4GWG \| pdb_00004gwg	Download File View File

Crystal Structure Analysis of 6-phosphogluconate dehydrogenase apo-form

He, C., Zhou, L., Zhang, L.

(2012) Cancer Cell 22: 585-600

Released	2012-11-28
Method	X-RAY DIFFRACTION 1.3907 Å
Organisms	Homo sapiens
Macromolecule	6-phosphogluconate dehydrogenase, decarboxylating (protein)
Unique Ligands	MES

Explore in 3D

4GWK \| pdb_00004gwk	Download File View File

Crystal structure of 6-phosphogluconate dehydrogenase complexed with 3-phosphoglyceric acid

He, C., Zhou, L., Zhang, L.

(2012) Cancer Cell 22: 585-600

Released	2012-11-28
Method	X-RAY DIFFRACTION 1.534 Å
Organisms	Homo sapiens
Macromolecule	6-phosphogluconate dehydrogenase, decarboxylating (protein)
Unique Ligands	3PG, MES

Explore in 3D

4IX7 \| pdb_00004ix7	Download File View File

Crystal Structure of the insv-BEN domain complexed to its DNA target site

Ren, A., Serganov, A., Patel, D.J.

(2013) Genes Dev 27: 602-614

Released	2013-03-20
Method	X-RAY DIFFRACTION 1.581 Å
Organisms	Drosophila melanogaster
Macromolecule	RE55538p (protein) 5'-D(GPTPTPCPCPAPAPTPTPGPGPAP*A)-3' (nucleic acid)

Explore in 3D

4X0G \| pdb_00004x0g	Download File View File

Structure of Bsg25A binding with DNA

Ren, A.

(2015) Genes Dev 29: 48-62

Released	2015-01-21
Method	X-RAY DIFFRACTION 3.2065 Å
Organisms	Drosophila melanogaster
Macromolecule	Blastoderm-specific gene 25A (protein) DNA (5'-D(GPTPTPCPCPAPAPTPTPGPGPAP*A)-3') (nucleic acid)
Unique Ligands	ACT

Explore in 3D

5ZAS \| pdb_00005zas	Download File View File

Crystal structure of 5-formylcytosine containing decamer dsDNA

Fu, T.R., Zhang, L.

(2019) Chem Sci 10: 7407-7417

Released	2019-02-13
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Homo sapiens
Macromolecule	DNA (5'-D(CPCPAPGP(5FC)PGPCPTPGPG)-3') (nucleic acid)
Unique Ligands	BCT

Explore in 3D

5ZAT \| pdb_00005zat	Download File View File

Crystal structure of 5-carboxylcytosine containing decamer dsDNA

Fu, T.R., Zhang, L.

(2019) Chem Sci 10: 7407-7417

Released	2019-02-13
Method	X-RAY DIFFRACTION 1.06 Å
Organisms	Homo sapiens
Macromolecule	DNA (5'-D(CPCPAPGP(CAC)PGPCPTPGPG)-3') (nucleic acid)

Explore in 3D

6JV3 \| pdb_00006jv3	Download File View File

Crystal structure of 5-hydoxylmethylcytosine containing decamer dsDNA

Zhang, L., Wang, Y.X.

(2019) Chem Sci 10: 7407-7417

Released	2019-07-31
Method	X-RAY DIFFRACTION 2.851 Å
Organisms	Homo sapiens
Macromolecule	DNA (5'-D(CPCPAPGP(5HC)PGPCPTPGPG)-3') (nucleic acid)

Explore in 3D

6JV5 \| pdb_00006jv5	Download File View File

Crystal structure of 5-methylcytosine containing decamer dsDNA

Zhang, L., Wang, Y.X.

(2019) Chem Sci 10: 7407-7417

Released	2019-07-31
Method	X-RAY DIFFRACTION 1.401 Å
Organisms	Homo sapiens
Macromolecule	DNA (5'-D(CPCPAPGP(5CM)PGPCPTPGPG)-3') (nucleic acid)

Explore in 3D

6R47 \| pdb_00006r47	Download File View File

The structure of pistol ribozyme bound to magnesium

Lilley, D.M.J., Wilson, T.M., Liu, Y.

(2019) J Am Chem Soc 141: 7865-7875

Released	2019-07-03
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Alistipes putredinis
Macromolecule	RNA (nucleic acid) RNA (50-MER) (nucleic acid)
Unique Ligands	MG

Explore in 3D

6U15 \| pdb_00006u15	Download File View File

Human thymine DNA glycosylase N140A mutant bound to DNA with 2'-F-5-carboxyl-dC substrate analog

Pidugu, L.S., Pozharski, E., Drohat, A.C.

(2019) J Am Chem Soc 141: 18851-18861

Released	2019-11-20
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	G/T mismatch-specific thymine DNA glycosylase (protein) DNA (28-MER) (nucleic acid)

Explore in 3D

6U16 \| pdb_00006u16	Download File View File

Human thymine DNA glycosylase N140A mutant bound to DNA with 5-carboxyl-dC substrate

Pidugu, L.S., Pozharski, E., Drohat, A.C.

(2019) J Am Chem Soc 141: 18851-18861

Released	2019-11-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	G/T mismatch-specific thymine DNA glycosylase (protein) DNA (28-MER) (nucleic acid)
Unique Ligands	EDO

Explore in 3D

6U17 \| pdb_00006u17	Download File View File

Human thymine DNA glycosylase bound to DNA with 2'-F-5-carboxyl-dC substrate analog

Pidugu, L.S., Pozharski, E., Drohat, A.C.

(2019) J Am Chem Soc 141: 18851-18861

Released	2019-11-20
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	G/T mismatch-specific thymine DNA glycosylase (protein) DNA (28-MER) (nucleic acid) DNA (30-MER) (nucleic acid)
Unique Ligands	ACT

1 to 25 of 35 Structures

Page 1 of 2

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

1FYG | pdb_00001fyg

2DPQ | pdb_00002dpq

2DPR | pdb_00002dpr

3O1M | pdb_00003o1m

3O1O | pdb_00003o1o

3O1P | pdb_00003o1p

3O1R | pdb_00003o1r

3O1S | pdb_00003o1s

3O1T | pdb_00003o1t

3O1U | pdb_00003o1u

3O1V | pdb_00003o1v

3UO7 | pdb_00003uo7

3UOB | pdb_00003uob

4GWG | pdb_00004gwg

4GWK | pdb_00004gwk

4IX7 | pdb_00004ix7

4X0G | pdb_00004x0g

5ZAS | pdb_00005zas

5ZAT | pdb_00005zat

6JV3 | pdb_00006jv3

6JV5 | pdb_00006jv5

6R47 | pdb_00006r47

6U15 | pdb_00006u15

6U16 | pdb_00006u16

6U17 | pdb_00006u17