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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, J.H."

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Search Summary

This query matches 510 Structures.

Refinements

Structure Determination Methodology

experimental (510)

Scientific Name of Source Organism

	Homo sapiens (291)
	Arabidopsis thaliana (45)
	Mus musculus (34)
	Rattus norvegicus (32)
	synthetic construct (31)
	Human immunodeficiency virus 1 (28)
	Severe acute respiratory syndrome coronavirus 2 (24)
	Cricetus cricetus (16)
	Gallus gallus (9)
	Sus scrofa (9)

More...

Taxonomy

	Eukaryota (427)
	Riboviria (67)
	Bacteria (56)
	other sequences (31)
	Duplodnaviria (12)
	Archaea (6)
	Eukaryota (eukaryotes) (4)
	unclassified sequences (4)
	Monodnaviria (2)
	Varidnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (323)
	ELECTRON MICROSCOPY (179)
	SOLUTION NMR (8)

Polymer Entity Type

	Protein (506)
	DNA (24)
	RNA (19)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (23)
	1.5 - 2.0 (75)
	2.0 - 2.5 (118)
	2.5 - 3.0 (96)
	3.0 - 3.5 (115)
	3.5 - 4.0 (43)
	4.0 - 4.5 (12)
	> 4.5 (19)

Release Date

	2000 - 2004 (24)
	2005 - 2009 (21)
	2010 - 2014 (53)
	2015 - 2019 (134)
	2020 - 2024 (240)
	2025 - 2029 (38)

Enzyme Classification Name

	Hydrolases (110)
	Transferases (67)
	Oxidoreductases (23)
	Isomerases (16)
	Ligases (12)
	Lyases (9)

Membrane Protein Annotation

	PDBTM (116)
	mpstruc (73)
	MemProtMD (53)
	OPM (41)

Symmetry Type

	Asymmetric (355)
	Cyclic (131)
	Dihedral (19)
	Icosahedral (2)
	Octahedral (2)

SCOP Classification

	Alpha and beta proteins (a/b) (60)
	All beta proteins (52)
	Alpha and beta proteins (a+b) (33)
	Artifacts (33)
	Coiled coil proteins (5)
	All alpha proteins (16)
	Small proteins (5)
	Low resolution protein structures (1)
	Multi-domain proteins (alpha and beta) (1)
	Membrane and cell surface proteins and peptides (1)

AllSelected

1 to 25 of 510 Structures

Page 1 of 21

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1DO8 \| pdb_00001do8	Download File View File

CRYSTAL STRUCTURE OF A CLOSED FORM OF HUMAN MITOCHONDRIAL NAD(P)+-DEPENDENT MALIC ENZYME

Yang, Z., Floyd, D.L., Loeber, G., Tong, L.

(2000) Nat Struct Biol 7: 251-257

Released	2000-03-06
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	MALIC ENZYME (protein)
Unique Ligands	MN, NAD, OXL

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1EFK \| pdb_00001efk	Download File View File

STRUCTURE OF HUMAN MALIC ENZYME IN COMPLEX WITH KETOMALONATE

Yang, Z., Floyd, D.L., Loeber, G., Tong, L.

(2000) Nat Struct Biol 7: 251-257

Released	2000-03-08
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	MALIC ENZYME (protein)
Unique Ligands	MAK, MG, NAD

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1EFL \| pdb_00001efl	Download File View File

HUMAN MALIC ENZYME IN A QUATERNARY COMPLEX WITH NAD, MG, AND TARTRONATE

Yang, Z., Floyd, D.L., Loeber, G., Tong, L.

(2000) Nat Struct Biol 7: 251-257

Released	2000-03-08
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	MALIC ENZYME (protein)
Unique Ligands	MG, NAD, TTN

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1EI3 \| pdb_00001ei3	Download File View File

CRYSTAL STRUCTURE OF NATIVE CHICKEN FIBRINOGEN

Yang, Z., Mochalkin, I., Veerapandian, L., Riley, M., Doolittle, R.F.

(2000) Proc Natl Acad Sci U S A 97: 3907-3912

Released	2000-05-10
Method	X-RAY DIFFRACTION 5.5 Å
Organisms	Gallus gallus
Macromolecule	FIBRINOGEN (protein)

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1GQ2 \| pdb_00001gq2	Download File View File

Malic Enzyme from Pigeon Liver

Yang, Z., Zhang, H., Liang, T.

(2002) Protein Sci 11: 332

Released	2002-05-23
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Columba livia
Macromolecule	MALIC ENZYME (protein)
Unique Ligands	CL, MN, NA, NAP, OXL

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1GZ3 \| pdb_00001gz3	Download File View File

Molecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate

Yang, Z., Lanks, C.W., Tong, L.

(2002) Structure 10: 951-960

Released	2003-05-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent malic enzyme, mitochondrial (protein)
Unique Ligands	ATP, FUM, MN, OXL

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1GZ4 \| pdb_00001gz4	Download File View File

molecular mechanism of the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate

Yang, Z., Lanks, C.W., Tong, L.

(2002) Structure 10: 951

Released	2002-07-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	NAD-DEPENDENT MALIC ENZYME (protein)
Unique Ligands	ATP, FUM, MN, TTN

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1H2H \| pdb_00001h2h	Download File View File

Crystal structure of TM1643

Yang, Z., Savchenko, A., Edwards, A., Arrowsmith, C., Tong, L., Northeast Structural Genomics Consortium (NESG)

(2003) J Biological Chem 278: 8804-8808

Released	2002-08-15
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Thermotoga maritima
Macromolecule	HYPOTHETICAL PROTEIN TM1643 (protein)
Unique Ligands	NAD

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1LWU \| pdb_00001lwu	Download File View File

Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide

Yang, Z., Spraggon, G., Pandi, L., Everse, S.J., Riley, M., Doolittle, R.F.

(2002) Biochemistry 41: 10218-10224

Released	2002-08-23
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Petromyzon marinus
Macromolecule	Fibrinogen alpha-1 chain (protein) Fibrinogen beta chain (protein) Fibrinogen gamma chain (protein) Peptide Ligand Gly-His-Arg-Pro-NH2 (protein)
Unique Ligands	BMA, CA, GAL, MAN, NAG, NDG
Unique branched monosaccharides	NAG

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1M1J \| pdb_00001m1j	Download File View File

Crystal structure of native chicken fibrinogen with two different bound ligands

Yang, Z., Kollman, J.M., Pandi, L., Doolittle, R.F.

(2001) Biochemistry 40: 12515-12523

Released	2002-06-26
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Gallus gallus
Macromolecule	Fibrinogen alpha subunit (protein) Fibrinogen beta chain (protein) Fibrinogen gamma chain (protein) GLY-HIS-ARG-PRO peptide (protein) GLY-PRO-ARG-PRO peptide (protein)
Unique Ligands	CA, NAG, NDG

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1N73 \| pdb_00001n73	Download File View File

Fibrin D-Dimer, Lamprey complexed with the PEPTIDE LIGAND: GLY-HIS-ARG-PRO-AMIDE

Yang, Z., Pandi, L., Doolittle, R.F.

(2002) Biochemistry 41: 15610-15617

Released	2003-01-07
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens Petromyzon marinus
Macromolecule	Fibrin alpha-1 chain (protein) Fibrin beta chain (protein) Fibrin gamma chain (protein) peptide ligand: Gly-his-Arg-Pro-amide (protein)
Unique Ligands	CA, NAG

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1N86 \| pdb_00001n86	Download File View File

Crystal structure of human D-dimer from cross-linked fibrin complexed with GPR and GHRPLDK peptide ligands.

Yang, Z., Pandi, L., Doolittle, R.F.

(2002) Biochemistry 41: 15610-15617

Released	2003-01-07
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens
Macromolecule	Fibrin alpha/alpha-E chain (protein) Fibrin beta chain (protein) Fibrin gamma chain (protein) fibrin alpha chain peptide ligand fragment Gly-Pro-Arg (protein) fibrin beta chain peptide ligand fragment Gly-His-Arg-Pro-Leu-Asp-Lys (protein)
Unique Ligands	CA, MAN, NDG

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1N8E \| pdb_00001n8e	Download File View File

Fragment Double-D from Human Fibrin

Yang, Z., Pandi, L., Doolittle, R.F.

(2002) Biochemistry 41: 15610-15617

Released	2003-01-07
Method	X-RAY DIFFRACTION 4.5 Å
Organisms	Homo sapiens
Macromolecule	Fibrin alpha/alpha-E chain (protein) Fibrin beta chain (protein) Fibrin gamma chain (protein)

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1OD2 \| pdb_00001od2	Download File View File

Acetyl-CoA Carboxylase Carboxyltransferase Domain

Zhang, H., Yang, Z., Shen, Y., Tong, L.

(2003) Science 299: 2064-2067

Released	2003-04-03
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ACETYL-COENZYME A CARBOXYLASE (protein)
Unique Ligands	ACO, ADE

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1OD4 \| pdb_00001od4	Download File View File

Acetyl-CoA Carboxylase Carboxyltransferase Domain

Zhang, H., Yang, Z., Shen, Y., Tong, L.

(2003) Science 299: 2064-2067

Released	2003-04-03
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ACETYL-COENZYME A CARBOXYLASE (protein)
Unique Ligands	ADE

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1PEG \| pdb_00001peg	Download File View File

Structural basis for the product specificity of histone lysine methyltransferases

Zhang, X., Yang, Z., Khan, S.I., Horton, J.R., Tamaru, H., Selker, E.U., Cheng, X.

(2003) Mol Cell 12: 177-185

Released	2003-08-05
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Homo sapiens Neurospora crassa
Macromolecule	Histone H3 (protein) histone H3 methyltransferase DIM-5 (protein)
Unique Ligands	SAH, ZN

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1PJ2 \| pdb_00001pj2	Download File View File

Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate malate, cofactor NADH, Mn++, and allosteric activator fumarate

Tao, X., Yang, Z., Tong, L.

(2003) Structure 11: 1141-1150

Released	2003-11-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent malic enzyme, mitochondrial (protein)
Unique Ligands	FUM, LMR, MN, NAI

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1PJ3 \| pdb_00001pj3	Download File View File

Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate pyruvate, cofactor NAD+, Mn++, and allosteric activator fumarate.

Tao, X., Yang, Z., Tong, L.

(2003) Structure 11: 1141-1150

Released	2003-11-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent malic enzyme, mitochondrial (protein)
Unique Ligands	FUM, MN, NAD, PYR

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1PJ4 \| pdb_00001pj4	Download File View File

Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate malate, ATP, Mn++, and allosteric activator fumarate.

Tao, X., Yang, Z., Tong, L.

(2003) Structure 11: 1141-1150

Released	2003-09-30
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent malic enzyme, mitochondrial (protein)
Unique Ligands	ATP, FUM, MLT, MN

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1PJL \| pdb_00001pjl	Download File View File

Crystal structure of human m-NAD-ME in ternary complex with NAD and Lu3+

Yang, Z., Batra, R., Floyd, D.L., Hung, H.-C., Chang, G.-G., Tong, L.

(2000) Biochem Biophys Res Commun 274: 440-444

Released	2003-06-17
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent malic enzyme, mitochondrial (protein)
Unique Ligands	LU, NAD

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1Q0S \| pdb_00001q0s	Download File View File

Binary Structure of T4DAM with AdoHcy

Yang, Z., Horton, J.R., Zhou, L., Zhang, X.J., Dong, A., Zhang, X., Schlagman, S.L., Kossykh, V., Hattman, S., Cheng, X.

(2003) Nat Struct Biol 10: 849-855

Released	2003-09-23
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Tequatrovirus T4
Macromolecule	DNA adenine methylase (protein)
Unique Ligands	SAH

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1Q0T \| pdb_00001q0t	Download File View File

Ternary Structure of T4DAM with AdoHcy and DNA

Yang, Z., Horton, J.R., Zhou, L., Zhang, X.J., Dong, A., Zhang, X., Schlagman, S.L., Kossykh, V., Hattman, S., Cheng, X.

(2003) Nat Struct Biol 10: 849-855

Released	2003-09-23
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Tequatrovirus T4
Macromolecule	DNA adenine methylase (protein) 5'-D(APCPAPGPGPAPTPCPCPTPGPT)-3' (nucleic acid)
Unique Ligands	IOD, SAH

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1T43 \| pdb_00001t43	Download File View File

Crystal Structure Analysis of E.coli Protein (N5)-Glutamine Methyltransferase (HemK)

Yang, Z., Shipman, L., Zhang, M., Anton, B.P., Roberts, R.J., Cheng, X.

(2004) J Mol Biology 340: 695-706

Released	2004-06-29
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Escherichia coli
Macromolecule	Protein methyltransferase hemK (protein)
Unique Ligands	SAH

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1U2Z \| pdb_00001u2z	Download File View File

Crystal structure of histone K79 methyltransferase Dot1p from yeast

Sawada, K., Yang, Z., Horton, J.R., Collins, R.E., Zhang, X., Cheng, X.

(2004) J Biological Chem 279: 43296-43306

Released	2004-09-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Histone-lysine N-methyltransferase, H3 lysine-79 specific (protein)
Unique Ligands	SAH

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1YF3 \| pdb_00001yf3	Download File View File

T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making Non- and Semi-specific (~1/4) Contact

Horton, J.R., Liebert, K., Hattman, S., Jeltsch, A., Cheng, X.

(2005) Cell 121: 349-361

Released	2005-05-17
Method	X-RAY DIFFRACTION 2.29 Å
Organisms	Tequatrovirus T4
Macromolecule	DNA adenine methylase (protein) 5'-D(APCPCPAPTPGPAPTPCPTPGPAPC)-3' (nucleic acid) 5'-D(TPGPTPCPAPGPAPTPCPAPTPGPG)-3' (nucleic acid)
Unique Ligands	GOL, SAH

1 to 25 of 510 Structures

Page 1 of 21

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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

1DO8 | pdb_00001do8

1EFK | pdb_00001efk

1EFL | pdb_00001efl

1EI3 | pdb_00001ei3

1GQ2 | pdb_00001gq2

1GZ3 | pdb_00001gz3

1GZ4 | pdb_00001gz4

1H2H | pdb_00001h2h

1LWU | pdb_00001lwu

1M1J | pdb_00001m1j

1N73 | pdb_00001n73

1N86 | pdb_00001n86

1N8E | pdb_00001n8e

1OD2 | pdb_00001od2

1OD4 | pdb_00001od4

1PEG | pdb_00001peg

1PJ2 | pdb_00001pj2

1PJ3 | pdb_00001pj3

1PJ4 | pdb_00001pj4

1PJL | pdb_00001pjl

1Q0S | pdb_00001q0s

1Q0T | pdb_00001q0t

1T43 | pdb_00001t43

1U2Z | pdb_00001u2z

1YF3 | pdb_00001yf3