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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Asano, Y."

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Search Summary

This query matches 133 Structures.

Refinements

Structure Determination Methodology

experimental (133)

Scientific Name of Source Organism

	Homo sapiens (33)
	Rattus norvegicus (27)
	synthetic construct (13)
	Rhodospirillum rubrum ATCC 11170 (10)
	Zea mays (10)
	Pseudomonas putida KT2440 (7)
	Haloferax tailed virus 1 (5)
	Bacillus cereus (4)
	Escherichia coli K-12 (4)
	Marinitoga sp. 1155 (4)

More...

Taxonomy

	Eukaryota (87)
	Bacteria (36)
	other sequences (13)
	Riboviria (11)
	Duplodnaviria (5)
	unclassified sequences (4)

Experimental Method

	X-RAY DIFFRACTION (84)
	ELECTRON MICROSCOPY (45)
	SOLUTION NMR (4)

Polymer Entity Type

	Protein (130)
	DNA (15)
	RNA (8)

Refinement Resolution (Å)

	1.0 - 1.5 (12)
	1.5 - 2.0 (25)
	2.0 - 2.5 (27)
	2.5 - 3.0 (32)
	3.0 - 3.5 (17)
	3.5 - 4.0 (13)
	> 4.5 (3)

Release Date

	1995 - 1999 (3)
	2000 - 2004 (4)
	2005 - 2009 (5)
	2010 - 2014 (8)
	2015 - 2019 (33)
	2020 - 2024 (77)
	2025 - 2029 (3)

Enzyme Classification Name

	Hydrolases (49)
	Transferases (5)
	Oxidoreductases (2)
	Isomerases (1)

Membrane Protein Annotation

	PDBTM (36)
	mpstruc (32)
	MemProtMD (28)
	OPM (19)

Symmetry Type

	Asymmetric (64)
	Cyclic (46)
	Dihedral (21)
	Helical (2)

SCOP Classification

	Alpha and beta proteins (a/b) (11)
	Alpha and beta proteins (a+b) (13)
	All beta proteins (6)
	Artifacts (3)
	All alpha proteins (2)

AllSelected

1 to 25 of 133 Structures

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1ATL \| pdb_00001atl	Download File View File

Structural interaction of natural and synthetic inhibitors with the VENOM METALLOPROTEINASE, ATROLYSIN C (FORM-D)

Zhang, D., Botos, I., Gomis-Rueth, F.-X., Doll, R., Blood, C., Njoroge, F.G., Fox, J.W., Bode, W., Meyer, E.F.

(1994) Proc Natl Acad Sci U S A 91: 8447-8451

Released	1995-10-15
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Crotalus atrox
Macromolecule	Snake venom metalloproteinase atrolysin-D (protein)
Unique Ligands	0QI, CA, ZN

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1DTH \| pdb_00001dth	Download File View File

METALLOPROTEASE

Botos, I., Scapozza, L., Zhang, D., Liotta, L.A., Meyer, E.F.

(1996) Proc Natl Acad Sci U S A 93: 2749-2754

Released	1997-02-12
Method	X-RAY DIFFRACTION 2 Å
Organisms	Crotalus atrox
Macromolecule	ATROLYSIN C (protein)
Unique Ligands	BAT, CA, ZN

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1HTD \| pdb_00001htd	Download File View File

STRUCTURAL INTERACTION OF NATURAL AND SYNTHETIC INHIBITORS WITH THE VENOM METALLOPROTEINASE, ATROLYSIN C (HT-D)

Zhang, D., Botos, I., Gomis-Rueth, F.-X., Doll, R., Blood, C., Njoroge, F.G., Fox, J.W., Bode, W., Meyer, E.F.

(1994) Proc Natl Acad Sci U S A 91: 8447-8451

Released	1995-09-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Crotalus atrox
Macromolecule	ATROLYSIN C (protein)
Unique Ligands	CA, ZN

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1HYN \| pdb_00001hyn	Download File View File

CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF HUMAN ERYTHROCYTE BAND-3 PROTEIN

Zhang, D., Kiyatkin, A., Bolin, J.T., Low, P.S.

(2000) Blood 96: 2925-2933

Released	2001-05-16
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	BAND 3 ANION TRANSPORT PROTEIN (protein)

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1KS4 \| pdb_00001ks4	Download File View File

The structure of Aspergillus niger endoglucanase-palladium complex

Khademi, S., Zhang, D., Swanson, S.M., Wartenberg, A., Witte, C., Meyer, E.F.

(2002) Acta Crystallogr D Biol Crystallogr 58: 660-667

Released	2003-01-21
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Aspergillus niger
Macromolecule	Endoglucanase A (protein)
Unique Ligands	PD

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1KS5 \| pdb_00001ks5	Download File View File

Structure of Aspergillus niger endoglucanase

Khademi, S., Zhang, D., Swanson, S.M., Wartenberg, A., Witte, C., Meyer, E.F.

(2002) Acta Crystallogr D Biol Crystallogr 58: 660-667

Released	2003-01-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Aspergillus niger
Macromolecule	Endoglucanase A (protein)

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1U6D \| pdb_00001u6d	Download File View File

Crystal structure of the Kelch domain of human Keap1

Li, X., Zhang, D., Hannink, M., Beamer, L.J.

(2004) J Biological Chem 279: 54750-54758

Released	2004-10-12
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	kelch-like ECH-associated protein 1 (protein)

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2HNG \| pdb_00002hng	Download File View File

The Crystal Structure of Protein of Unknown Function SP1558 from Streptococcus pneumoniae

Kim, Y., Zhang, D., Zhou, M., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

(2006) To be published

Released	2006-08-15
Method	X-RAY DIFFRACTION 1.63 Å
Organisms	Streptococcus pneumoniae TIGR4
Macromolecule	Hypothetical protein (protein)

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2JY5 \| pdb_00002jy5	Download File View File

NMR structure of Ubiquilin 1 UBA domain

Zhang, D., Raasi, S., Fushman, D.

(2008) J Mol Biology 377: 162-180

Released	2008-03-18
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Ubiquilin-1 (protein)

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2JY6 \| pdb_00002jy6	Download File View File

Solution structure of the complex of ubiquitin and ubiquilin 1 UBA domain

Zhang, D., Raasi, S., Fushman, D.

(2008) J Mol Biology 377: 162-180

Released	2008-03-18
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Ubiquilin-1 (protein) Ubiquitin protein (protein)

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2MR9 \| pdb_00002mr9	Download File View File

NMR structure of UBA domain of DNA-damage-inducible 1 protein (Ddi1)

Zhang, D., Fushman, D.

(2015) Structure 23: 542-557

Released	2015-02-04
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	DNA damage-inducible protein 1 (protein)

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2MRO \| pdb_00002mro	Download File View File

Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1)

Zhang, D., Fushman, D.

(2015) Structure 23: 542-557

Released	2015-02-04
Method	SOLUTION NMR
Organisms	Homo sapiens Saccharomyces cerevisiae S288C
Macromolecule	DNA damage-inducible protein 1 (protein) Polyubiquitin-B (protein)

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2W0J \| pdb_00002w0j	Download File View File

Crystal structure of Chk2 in complex with NSC 109555, a specific inhibitor

Lountos, G.T., Tropea, J.E., Zhang, D., Jobson, A.G., Pommier, Y., Shoemaker, R.H., Waugh, D.S.

(2009) Protein Sci 18: 92

Released	2009-02-10
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE CHK2 (protein)
Unique Ligands	NO3, ZAT

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3FCX \| pdb_00003fcx	Download File View File

Crystal structure of human esterase D

Wu, D., Li, Y., Song, G., Zhang, D., Shaw, N., Liu, Z.J.

(2009) FASEB J 23: 1441-1446

Released	2008-12-09
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	S-formylglutathione hydrolase (protein)
Unique Ligands	CA, MG

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3JCD \| pdb_00003jcd	Download File View File

Structure of Escherichia coli EF4 in posttranslocational ribosomes (Post EF4)

Zhang, D., Yan, K., Liu, G., Song, G., Luo, J., Shi, Y., Cheng, E., Wu, S., Jiang, T., Low, J., Gao, N., Qin, Y.

(2016) Nat Struct Mol Biol 23: 125-131

Released	2016-01-13
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Escherichia coli K-12 synthetic construct
Macromolecule	Unique protein chains: 51 Unique nucleic acid chains: 5

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3JCE \| pdb_00003jce	Download File View File

Structure of Escherichia coli EF4 in pretranslocational ribosomes (Pre EF4)

Zhang, D., Yan, K., Liu, G., Song, G., Luo, J., Shi, Y., Cheng, E., Wu, S., Jiang, T., Low, J., Gao, N., Qin, Y.

(2016) Nat Struct Mol Biol 23: 125-131

Released	2016-01-13
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Escherichia coli K-12 synthetic construct
Macromolecule	Unique protein chains: 51 Unique nucleic acid chains: 6
Unique Ligands	GNP, MG, PHE

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3NS8 \| pdb_00003ns8	Download File View File

Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5

Zhang, D., LaRonde-LeBlanc, N., Fushman, D.

(2012) Biochim Biophys Acta 1823: 2046-2056

Released	2011-07-20
Method	X-RAY DIFFRACTION 1.707 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin (protein)
Unique Ligands	EPE, GOL

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3P2M \| pdb_00003p2m	Download File View File

Crystal Structure of a Novel Esterase Rv0045c from Mycobacterium tuberculosis

Zheng, X.D., Guo, J., Xu, L., Li, H., Zhang, D., Zhang, K., Sun, F., Wen, T., Liu, S., Pang, H.

(2011) PLoS One 6: e20506-e20506

Released	2011-07-06
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	POSSIBLE HYDROLASE (protein)

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4FZ3 \| pdb_00004fz3	Download File View File

Crystal structure of SIRT3 in complex with acetyl p53 peptide coupled with 4-amino-7-methylcoumarin

Liu, D., Wu, J., Zhang, D., Chen, K., Jiang, H., Liu, H.

(2013) J Med Chem 56: 761-780

Released	2013-03-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacetylase sirtuin-3, mitochondrial (protein) peptide from Cellular tumor antigen p53 (protein)
Unique Ligands	ZN

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4M3Q \| pdb_00004m3q	Download File View File

Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor UNC1917

Zhang, W., Zhang, D., Stashko, M.A., DeRyckere, D., Hunter, D., Kireev, D.B., Miley, M., Cummings, C., Lee, M., Norris-Drouin, J., Stewart, W.M., Sather, S., Zhou, Y., Kirkpatrick, G., Machius, M., Janzen, W.P., Earp, H.S., Graham, D.K., Frye, S., Wang, X.

(2013) J Med Chem 56: 9683-9692

Released	2013-11-27
Method	X-RAY DIFFRACTION 2.718 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase Mer (protein)
Unique Ligands	24K, CL, MG

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4NTJ \| pdb_00004ntj	Download File View File

Structure of the human P2Y12 receptor in complex with an antithrombotic drug

Zhang, K., Zhang, J., Gao, Z.-G., Zhang, D., Zhu, L., Han, G.W., Moss, S.M., Paoletta, S., Kiselev, E., Lu, W., Fenalti, G., Zhang, W., Muller, C.E., Yang, H., Jiang, H., Cherezov, V., Katritch, V., Jacobson, K.A., Stevens, R.C., Wu, B., Zhao, Q., GPCR Network (GPCR)

(2014) Nature 509: 115-118

Released	2014-03-26
Method	X-RAY DIFFRACTION 2.62 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12 (protein)
Unique Ligands	AZJ, CLR, OLC

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4PXZ \| pdb_00004pxz	Download File View File

Crystal structure of P2Y12 receptor in complex with 2MeSADP

Zhang, J., Zhang, K., Gao, Z.G., Paoletta, S., Zhang, D., Han, G.W., Li, T., Ma, L., Zhang, W., Muller, C.E., Yang, H., Jiang, H., Cherezov, V., Katritch, V., Jacobson, K.A., Stevens, R.C., Wu, B., Zhao, Q., GPCR Network (GPCR)

(2014) Nature 509: 119-122

Released	2014-04-30
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	P2Y purinoceptor 12, Soluble cytochrome b562 (protein)
Unique Ligands	6AD, CLR, OLC, PEG

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4PY0 \| pdb_00004py0	Download File View File

Crystal structure of P2Y12 receptor in complex with 2MeSATP

(2014) Nature 509: 119-122

Released	2014-04-30
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	P2Y purinoceptor 12, Soluble cytochrome b562 (protein)
Unique Ligands	6AT, OLC

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4RIM \| pdb_00004rim	Download File View File

Native structure of intercalation-locked DNA tetraplex

Tripathi, S.K., Zhang, D., Paukstelis, P.

(2015) Nucleic Acids Res 43: 1937-1944

Released	2015-02-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	synthetic construct
Macromolecule	DNA (5'-D(APCPTPCPGPGPAPTPGPAP*T)-3') (nucleic acid)

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4RIP \| pdb_00004rip	Download File View File

BromoUracil substituted structure of intercalation-locked DNA tetraplex

Tripathi, S.K., Zhang, D., Paukstelis, P.

(2015) Nucleic Acids Res 43: 1937-1944

Released	2015-02-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	synthetic construct
Macromolecule	DNA (5'-D(APCP(BRU)PCPGPGPAP(BRU)PGPAP*T)-3') (nucleic acid)

1 to 25 of 133 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

1ATL | pdb_00001atl

1DTH | pdb_00001dth

1HTD | pdb_00001htd

1HYN | pdb_00001hyn

1KS4 | pdb_00001ks4

1KS5 | pdb_00001ks5

1U6D | pdb_00001u6d

2HNG | pdb_00002hng

2JY5 | pdb_00002jy5

2JY6 | pdb_00002jy6

2MR9 | pdb_00002mr9

2MRO | pdb_00002mro

2W0J | pdb_00002w0j

3FCX | pdb_00003fcx

3JCD | pdb_00003jcd

3JCE | pdb_00003jce

3NS8 | pdb_00003ns8

3P2M | pdb_00003p2m

4FZ3 | pdb_00004fz3

4M3Q | pdb_00004m3q

4NTJ | pdb_00004ntj

4PXZ | pdb_00004pxz

4PY0 | pdb_00004py0

4RIM | pdb_00004rim

4RIP | pdb_00004rip