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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Park, S.-Y."

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Search Summary

This query matches 114 Structures.

Refinements

Structure Determination Methodology

experimental (114)

Scientific Name of Source Organism

	Physeter macrocephalus (25)
	Homo sapiens (23)
	Escherichia coli (12)
	Fusarium oxysporum (6)
	Thermus thermophilus (6)
	Arabidopsis thaliana (5)
	Haemophilus influenzae (5)
	Equus caballus (4)
	Influenza A virus (A/Puerto Rico/8/1934(H1N1)) (3)
	Mammuthus primigenius (3)

More...

Taxonomy

	Eukaryota (76)
	Bacteria (35)
	Riboviria (3)
	Eukaryota (eukaryotes) (2)

Experimental Method

X-RAY DIFFRACTION (114)

Polymer Entity Type

	Protein (114)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (40)
	1.5 - 2.0 (37)
	2.0 - 2.5 (26)
	2.5 - 3.0 (6)
	3.0 - 3.5 (4)
	3.5 - 4.0 (1)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (35)
	2005 - 2009 (65)
	2010 - 2014 (8)
	2015 - 2019 (4)

Enzyme Classification Name

	Oxidoreductases (41)
	Hydrolases (19)
	Transferases (7)
	Isomerases (4)
	Lyases (4)

Membrane Protein Annotation

	MemProtMD (2)
	PDBTM (2)
	mpstruc (1)

Symmetry Type

	Asymmetric (68)
	Cyclic (46)
	Dihedral (10)
	Tetrahedral (4)
	Octahedral (3)

SCOP Classification

	All alpha proteins (60)
	Alpha and beta proteins (a+b) (11)
	Alpha and beta proteins (a/b) (9)
	Multi-domain proteins (alpha and beta) (12)
	Artifacts (5)
	All beta proteins (4)
	Peptides (3)
	Membrane and cell surface proteins and peptides (2)

AllSelected

1 to 25 of 114 Structures

Page 1 of 5

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1D06 \| pdb_00001d06	Download File View File

STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION

Miyatake, H., Mukai, M., Park, S.-Y., Adachi, S., Tamura, K., Nakamura, H., Nakamura, K., Tsuchiya, T., Iizuka, T., Shiro, Y.

(2000) J Mol Biology 301: 415-431

Released	2000-03-15
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Sinorhizobium meliloti
Macromolecule	nitrogen fixation regulatory protein fixL (protein)
Unique Ligands	HEM

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1EW0 \| pdb_00001ew0	Download File View File

CRYSTAL STRUCTURE ANALYSIS OF THE SENSOR DOMAIN OF RMFIXL(FERROUS FORM)

Miyatake, H., Mukai, M., Park, S.-Y., Adachi, S., Tamura, K., Nakamura, H., Nakamura, K., Tsuchiya, T., Iizuka, T., Shiro, Y.

(2000) J Mol Biology 301: 415-431

Released	2000-05-10
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Sinorhizobium meliloti
Macromolecule	FIXL (protein)
Unique Ligands	HEM

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1F24 \| pdb_00001f24	Download File View File

CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ALA MUTANTS OF CYTOCHROME P450NOR

Shimizu, H., Park, S.-Y.

(2000) J Inorg Biochem 82: 103-111

Released	2000-11-23
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Fusarium oxysporum
Macromolecule	NITRIC OXIDE REDUCTASE (protein)
Unique Ligands	GOL, HEM, NO

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1F25 \| pdb_00001f25	Download File View File

CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ASN MUTANTS OF CYTOCHROME P450NOR

Shimizu, H., Park, S.-Y.

(2000) J Inorg Biochem 82: 103-111

Released	2000-11-23
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Fusarium oxysporum
Macromolecule	NITRIC OXIDE REDUCTASE (protein)
Unique Ligands	GOL, HEM, NO

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1F26 \| pdb_00001f26	Download File View File

CRYSTAL STRUCTURE OF NO COMPLEX OF THR243VAL MUTANTS OF CYTOCHROME P450NOR

Shimizu, H., Park, S.-Y.

(2000) J Inorg Biochem 82: 103-111

Released	2000-11-23
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Fusarium oxysporum
Macromolecule	NITRIC OXIDE REDUCTASE (protein)
Unique Ligands	GOL, HEM, NO

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1GED \| pdb_00001ged	Download File View File

A positive charge route for the access of nadh to heme formed in the distal heme pocket of cytochrome p450nor

Kudo, T., Takaya, N., Park, S.-Y., Shiro, Y., Shoun, H.

(2001) J Biological Chem 276: 5020-5026

Released	2000-11-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450 55A1 (protein)
Unique Ligands	BR, HEM

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1GEI \| pdb_00001gei	Download File View File

STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM

Lee, D.-S., Park, S.-Y., Yamane, K., Shiro, Y.

(2001) Biochemistry 40: 2669-2677

Released	2000-11-29
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450 55A1 (protein)
Unique Ligands	HEM, NBN

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1GEJ \| pdb_00001gej	Download File View File

STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM

lee, D.-S., Park, S.-Y., Yamane, K., Shiro, Y.

(2001) Biochemistry 40: 2669-2677

Released	2000-12-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Fusarium oxysporum
Macromolecule	CYTOCHROME P450 55A1 (protein)
Unique Ligands	HEM, NBN

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1IRD \| pdb_00001ird	Download File View File

Crystal Structure of Human Carbonmonoxy-Haemoglobin at 1.25 A Resolution

Park, S.-Y., Tame, J.R.H.

To be published

Released	2001-10-17
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha chain (protein) Hemoglobin beta chain (protein)
Unique Ligands	CMO, HEM

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1IT2 \| pdb_00001it2	Download File View File

Hagfish deoxy hemoglobin

Mito, M., Chong, K.T., Park, S.-Y., Tame, J.R.

(2002) J Biological Chem 277: 21898-21905

Released	2002-01-23
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Eptatretus burgeri
Macromolecule	hemoglobin (protein)
Unique Ligands	HEM

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1IT3 \| pdb_00001it3	Download File View File

Hagfish CO ligand hemoglobin

Mito, M., Chong, K.T., Park, S.-Y., Tame, J.R.

(2002) J Biological Chem 277: 21898-21905

Released	2002-01-23
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Eptatretus burgeri
Macromolecule	hemoglobin (protein)
Unique Ligands	CMO, HEM

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1IUJ \| pdb_00001iuj	Download File View File

The structure of TT1380 protein from thermus thermophilus

Wada, T., Shirouzu, M., Park, S.-Y., Tame, J.R.H., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Proteins 55: 778-780

Released	2003-09-09
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Thermus thermophilus
Macromolecule	hypothetical protein TT1380 (protein)
Unique Ligands	ZN

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1IWH \| pdb_00001iwh	Download File View File

Crystal Structure of Horse Carbonmonoxyhemoglobin-Bezafibrate Complex at 1.55A Resolution: A Novel Allosteric Binding Site in R-State Hemoglobin

Shibayama, N., Miura, S., Tame, J.R.H., Yonetani, T., Park, S.-Y.

(2002) J Biological Chem 277: 38791-38796

Released	2002-10-02
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Equus caballus
Macromolecule	Hemoglobin alpha chain (protein) Hemoglobin beta chain (protein)
Unique Ligands	CMO, HEM, PEM

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1IWI \| pdb_00001iwi	Download File View File

Putidaredoxin-Binding Stablilizes an Active Conformer of Cytochrome P450cam in its Reduced State; Crystal Structure of Cytochrome P450cam

Nagano, S., Shimada, H., Tarumi, A., Hishiki, T., Kimata-Ariga, Y., Egawa, T., Park, S.-Y., Adachi, S., Shiro, Y., Ishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Biochemistry 42: 14507-14514

Released	2002-06-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas putida
Macromolecule	CYTOCHROME P450-CAM (protein)
Unique Ligands	CAM, HEM

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1IWJ \| pdb_00001iwj	Download File View File

Putidaredoxin-Binding Stablilizes an Active Conformer of Cytochrome P450cam in its Reduced State; Crystal Structure of Mutant(109K) Cytochrome P450cam

Nagano, S., Shimada, H., Tarumi, A., Hishiki, T., Kimata-Ariga, Y., Egawa, T., Park, S.-Y., Adachi, S., Shiro, Y., Ishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Biochemistry 42: 14507-14514

Released	2002-06-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas putida
Macromolecule	CYTOCHROME P450-CAM (protein)
Unique Ligands	CAM, HEM

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1IWK \| pdb_00001iwk	Download File View File

Putidaredoxin-Binding Stablilizes an Active Conformer of Cytochrome P450cam in its Reduced State; Crystal Structure of Mutant(112K) Cytochrome P450cam

Nagano, S., Shimada, H., Tarumi, A., Hishiki, T., Kimata-Ariga, Y., Egawa, T., Park, S.-Y., Adachi, S., Shiro, Y., Ishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Biochemistry 42: 14507-14514

Released	2002-06-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas putida
Macromolecule	CYTOCHROME P450-CAM (protein)
Unique Ligands	HEM

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1J3M \| pdb_00001j3m	Download File View File

Crystal structure of the conserved hypothetical protein TT1751 from Thermus thermophilus HB8

Kishishita, S., Terada, T., Shirouzu, M., Kuramitsu, S., Park, S.-Y., Tame, R.H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Proteins 57: 883-887

Released	2004-05-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus
Macromolecule	the conserved hypothetical protein TT1751 (protein)
Unique Ligands	SO3

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1J3Y \| pdb_00001j3y	Download File View File

Direct observation of photolysis-induced tertiary structural changes in human hemoglobin; Crystal structure of alpha(Fe)-beta(Ni) hemoglobin (laser photolysed)

Adachi, S., Park, S.-Y., Tame, J.R.H., Shiro, Y., Shibayama, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Proc Natl Acad Sci U S A 100: 7039-7044

Released	2003-07-22
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha Chain (protein) Hemoglobin beta Chain (protein)
Unique Ligands	2FU, CMO, HEM, HNI

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1J3Z \| pdb_00001j3z	Download File View File

Direct observation of photolysis-induced tertiary structural changes in human haemoglobin; Crystal structure of alpha(Fe-CO)-beta(Ni) hemoglobin (laser unphotolysed)

Adachi, S., Park, S.-Y., Tame, J.R.H., Shiro, Y., Shibayama, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Proc Natl Acad Sci U S A 100: 7039-7044

Released	2003-07-22
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha Chain (protein) Hemoglobin beta Chain (protein)
Unique Ligands	2FU, CMO, HEM, HNI

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1J40 \| pdb_00001j40	Download File View File

Direct observation of photolysis-induced tertiary structural changes in human haemoglobin; Crystal structure of alpha(Ni)-beta(Fe-CO) hemoglobin (laser unphotolysed)

Adachi, S., Park, S.-Y., Tame, J.R.H., Shiro, Y., Shibayama, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Proc Natl Acad Sci U S A 100: 7039-7044

Released	2003-07-22
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha Chain (protein) Hemoglobin beta Chain (protein)
Unique Ligands	2FU, CMO, HEM, HNI

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1J41 \| pdb_00001j41	Download File View File

Direct observation of photolysis-induced tertiary structural changes in human haemoglobin; Crystal structure of alpha(Ni)-beta(Fe) hemoglobin (laser photolysed)

Adachi, S., Park, S.-Y., Tame, J.R.H., Shiro, Y., Shibayama, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Proc Natl Acad Sci U S A 100: 7039-7044

Released	2003-07-22
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin alpha Chain (protein) Hemoglobin beta Chain (protein)
Unique Ligands	2FU, CMO, HEM, HNI

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1QSH \| pdb_00001qsh	Download File View File

MAGNESIUM(II)-AND ZINC(II)-PROTOPORPHYRIN IX'S STABILIZE THE LOWEST OXYGEN AFFINITY STATE OF HUMAN HEMOGLOBIN EVEN MORE STRONGLY THAN DEOXYHEME

Miyazaki, G., Morimoto, H., Yun, K.-M., Park, S.-Y., Nakagawa, A., Minagawa, H., Shibayama, N.

(1999) J Mol Biology 292: 1121-1136

Released	1999-07-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN (HEMOGLOBIN ALPHA CHAIN) (protein) PROTEIN (HEMOGLOBIN BETA CHAIN) (protein)
Unique Ligands	HEG, HEM

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1QSI \| pdb_00001qsi	Download File View File

MAGNESIUM(II)-AND ZINC(II)-PROTOPORPHYRIN IX'S STABILIZE THE LOWEST OXYGEN AFFINITY STATE OF HUMAN HEMOGLOBIN EVEN MORE STRONGLY THAN DEOXYHEME

Miyazaki, G., Morimoto, H., Yun, K.-M., Park, S.-Y., Nakagawa, A., Minagawa, H., Shibayama, N.

(1999) J Mol Biology 292: 1121-1136

Released	1999-07-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN (HEMOGLOBIN ALPHA CHAIN) (protein) PROTEIN (HEMOGLOBIN BETA CHAIN) (protein)
Unique Ligands	CMO, HEG, HEM

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1UAN \| pdb_00001uan	Download File View File

Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8

Handa, N., Terada, T., Tame, J.R.H., Park, S.-Y., Kinoshita, K., Ota, M., Nakamura, H., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Protein Sci 12: 1621-1632

Released	2003-08-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus
Macromolecule	hypothetical protein TT1542 (protein)

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1UDT \| pdb_00001udt	Download File View File

Crystal structure of Human Phosphodiesterase 5 complexed with Sildenafil(Viagra)

Sung, B.-J., Lee, J.I., Heo, Y.-S., Kim, J.H., Moon, J., Yoon, J.M., Hyun, Y.-L., Kim, E., Eum, S.J., Lee, T.G., Cho, J.M., Park, S.-Y., Lee, J.-O., Jeon, Y.H., Hwang, K.Y., Ro, S.

(2003) Nature 425: 98-102

Released	2004-05-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	cGMP-specific 3',5'-cyclic phosphodiesterase (protein)
Unique Ligands	MG, VIA, ZN

1 to 25 of 114 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

1D06 | pdb_00001d06

1EW0 | pdb_00001ew0

1F24 | pdb_00001f24

1F25 | pdb_00001f25

1F26 | pdb_00001f26

1GED | pdb_00001ged

1GEI | pdb_00001gei

1GEJ | pdb_00001gej

1IRD | pdb_00001ird

1IT2 | pdb_00001it2

1IT3 | pdb_00001it3

1IUJ | pdb_00001iuj

1IWH | pdb_00001iwh

1IWI | pdb_00001iwi

1IWJ | pdb_00001iwj

1IWK | pdb_00001iwk

1J3M | pdb_00001j3m

1J3Y | pdb_00001j3y

1J3Z | pdb_00001j3z

1J40 | pdb_00001j40

1J41 | pdb_00001j41

1QSH | pdb_00001qsh

1QSI | pdb_00001qsi

1UAN | pdb_00001uan

1UDT | pdb_00001udt