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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Zhao, D."

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Search Summary

This query matches 62 Structures.

Refinements

Structure Determination Methodology

experimental (62)

Scientific Name of Source Organism

	Homo sapiens (51)
	Escherichia coli (3)
	Arabidopsis thaliana (2)
	Sus scrofa (2)
	Acidithiobacillus ferrooxidans (1)
	Camelus dromedarius (1)
	Escherichia coli str. K-12 substr. W3110 (1)
	Nepeta sibirica (1)
	Saccharomyces cerevisiae (1)
	Severe acute respiratory syndrome coronavirus 2 (1)

More...

Taxonomy

	Eukaryota (56)
	Bacteria (6)
	Riboviria (1)
	other sequences (1)

Experimental Method

	ELECTRON MICROSCOPY (42)
	X-RAY DIFFRACTION (16)
	SOLUTION NMR (4)

Polymer Entity Type

	Protein (62)
	DNA (34)
	RNA (6)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (4)
	2.0 - 2.5 (4)
	2.5 - 3.0 (12)
	3.0 - 3.5 (15)
	3.5 - 4.0 (15)
	4.0 - 4.5 (2)
	> 4.5 (4)

Release Date

	1995 - 1999 (5)
	2000 - 2004 (4)
	2010 - 2014 (3)
	2015 - 2019 (7)
	2020 - 2024 (43)

Enzyme Classification Name

	Transferases (35)
	Hydrolases (8)
	Isomerases (1)

Symmetry Type

	Asymmetric (55)
	Cyclic (7)
	Dihedral (2)

SCOP Classification

	All alpha proteins (7)
	Alpha and beta proteins (a+b) (8)
	Alpha and beta proteins (a/b) (4)
	Artifacts (4)
	All beta proteins (5)
	Small proteins (1)

AllSelected

1 to 25 of 62 Structures

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1A3Z \| pdb_00001a3z	Download File View File

REDUCED RUSTICYANIN AT 1.9 ANGSTROMS

Zhao, D., Shoham, M.

(1998) Biophys J 74: 233-233

Released	1998-07-29
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Acidithiobacillus ferrooxidans
Macromolecule	RUSTICYANIN (protein)
Unique Ligands	CU1

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1JAK \| pdb_00001jak	Download File View File

Streptomyces plicatus beta-N-acetylhexosaminidase in Complex with (2R,3R,4S,5R)-2-acetamido-3,4-dihydroxy-5-hydroxymethyl-piperidinium chloride (IFG)

Mark, B.L., Vocadlo, D.J., Zhao, D., Knapp, S., Withers, S.G., James, M.N.

(2001) J Biological Chem 276: 42131-42137

Released	2001-11-21
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Streptomyces plicatus
Macromolecule	Beta-N-acetylhexosaminidase (protein)
Unique Ligands	CL, GOL, IFG, SO4

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1NOU \| pdb_00001nou	Download File View File

Native human lysosomal beta-hexosaminidase isoform B

Mark, B.L., Mahuran, D.J., Cherney, M.M., Zhao, D., Knapp, S., James, M.N.G.

(2003) J Mol Biology 327: 1093-1109

Released	2003-04-08
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	beta-hexosaminidase beta chain (protein)
Unique Ligands	GOL, SO4
Unique branched monosaccharides	NAG

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1NOW \| pdb_00001now	Download File View File

Human lysosomal beta-hexosaminidase isoform B in complex with (2R,3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (GalNAc-isofagomine)

Mark, B.L., Mahuran, D.J., Cherney, M.M., Zhao, D., Knapp, S., James, M.N.G.

(2003) J Mol Biology 327: 1093-1109

Released	2003-04-29
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	beta-hexosaminidase beta chain (protein)
Unique Ligands	GOL, IFG, SO4
Unique branched monosaccharides	NAG

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1NP0 \| pdb_00001np0	Download File View File

Human lysosomal beta-hexosaminidase isoform B in complex with intermediate analogue NAG-thiazoline

Mark, B.L., Mahuran, D.J., Cherney, M.M., Zhao, D., Knapp, S., James, M.N.G.

(2003) J Mol Biology 327: 1093-1109

Released	2003-04-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Beta-hexosaminidase subunit beta (protein) Beta-hexosaminidase subunit beta chain A (protein) Beta-hexosaminidase subunit beta chain B (protein)
Unique Ligands	GOL, NGT, SO4
Unique branched monosaccharides	NAG

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1RCS \| pdb_00001rcs	Download File View File

NMR STUDY OF TRP REPRESSOR-OPERATOR DNA COMPLEX

Zhao, D., Zheng, Z.

(1994) J Mol Biology 238: 592-614

Released	1996-06-20
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	TRP REPRESSOR (protein) DNA (5'-D(CPGPTPAPCPTPAPGPTPTPAPAPCPTPAPGPTPAPCPG)-3') (nucleic acid)
Unique Ligands	TRP

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1WRS \| pdb_00001wrs	Download File View File

NMR STUDY OF HOLO TRP REPRESSOR

Zhao, D., Zheng, Z.

(1993) J Mol Biology 229: 735-746

Released	1996-06-20
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	HOLO TRP REPRESSOR (protein)
Unique Ligands	TRP

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1WRT \| pdb_00001wrt	Download File View File

NMR STUDY OF APO TRP REPRESSOR

Zhao, D., Zheng, Z.

(1993) J Mol Biology 229: 735-746

Released	1996-06-20
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	APO TRP REPRESSOR (protein)

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2MOX \| pdb_00002mox	Download File View File

solution structure of tandem SH3 domain of Sorbin and SH3 domain-containing protein 1

Zhao, D., Wang, C., Zhang, J., Wu, J., Shi, Y., Zhang, Z., Gong, Q.

(2014) J Struct Biol 187: 194-205

Released	2014-05-28
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Sorbin and SH3 domain-containing protein 1 (protein)

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3EIP \| pdb_00003eip	Download File View File

CRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO A RIBOSOME-INACTIVATING RNASE

Li, C., Zhao, D., Djebli, A., Shoham, M.

(1999) Structure 7: 1365-1372

Released	1999-11-10
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	PROTEIN (COLICIN E3 IMMUNITY PROTEIN) (protein)
Unique Ligands	ZN

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4LN2 \| pdb_00004ln2	Download File View File

The second SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin

Zhao, D., Li, F., Wu, J., Shi, Y., Zhang, Z., Gong, Q.

(2014) J Struct Biol 187: 194-205

Released	2014-05-28
Method	X-RAY DIFFRACTION 1 Å
Organisms	Homo sapiens
Macromolecule	Sorbin and SH3 domain-containing protein 1 (protein) proline rich peptide (protein)

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4LNP \| pdb_00004lnp	Download File View File

The first SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin

Zhao, D., Li, F., Wu, J., Shi, Y., Zhang, Z., Gong, Q.

(2014) J Struct Biol 187: 194-205

Released	2014-05-28
Method	X-RAY DIFFRACTION 1.41 Å
Organisms	Homo sapiens
Macromolecule	Sorbin and SH3 domain-containing protein 1 (protein) Vinculin (protein)

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4W5A \| pdb_00004w5a	Download File View File

Complex structure of ATRX ADD bound to H3K9me3S10ph peptide

Zhao, D., Xiang, B., Li, H.

(2015) Proc Natl Acad Sci U S A 112: 6820-6827

Released	2015-01-21
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Peptide from Histone H3.3 (protein) Transcriptional regulator ATRX (protein)
Unique Ligands	ZN

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5HJB \| pdb_00005hjb	Download File View File

AF9 YEATS in complex with histone H3 Crotonylation at K9

Li, Y.Y., Zhao, D., Guan, H.P., Li, H.T.

(2016) Mol Cell 62: 181-193

Released	2016-04-20
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Protein AF-9 (protein) peptide of Histone H3.1 (protein)

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5HJC \| pdb_00005hjc	Download File View File

BRD3 second bromodomain in complex with histone H3 acetylation at K18

Li, Y.Y., Zhao, D., Guan, H.P., Li, H.T.

(2016) Mol Cell 62: 181-193

Released	2016-04-20
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Bromodomain-containing protein 3 (protein) peptide of Histone H3.1 (protein)
Unique Ligands	CL, EDO

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5HJD \| pdb_00005hjd	Download File View File

AF9 YEATS in complex with histone H3 Crotonylation at K18

Li, Y.Y., Zhao, D., Guan, H.P., Li, H.T.

(2016) Mol Cell 62: 181-193

Released	2016-04-20
Method	X-RAY DIFFRACTION 2.806 Å
Organisms	Homo sapiens
Macromolecule	Protein AF-9 (protein) peptide of Histone H3.1 (protein)
Unique Ligands	CU, SO4

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5IQL \| pdb_00005iql	Download File View File

Crystal structure of YEATS2 YEATS bound to H3K27cr peptide

Li, H., Zhao, D., Guan, H.

(2016) Cell Res 26: 629-632

Released	2016-07-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Histone H3.1 (protein) YEATS domain-containing protein 2 (protein)

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5XNV \| pdb_00005xnv	Download File View File

Crystal structure of YEATS2 YEATS bound to H3K27ac peptide

Li, H.T., Guan, H.P., Zhao, D.

(2017) Nat Commun 8: 1088-1088

Released	2017-11-01
Method	X-RAY DIFFRACTION 2.696 Å
Organisms	Homo sapiens
Macromolecule	ALA-ALA-ARG-ALY-SER-ALA-PRO-ALA (protein) YEATS domain-containing protein 2 (protein)
Unique Ligands	CL, NH4

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5XTZ \| pdb_00005xtz	Download File View File

Crystal structure of GAS41 YEATS bound to H3K27ac peptide

Li, H.T., Zhao, D.

(2018) Cell Discov 4: 28-28

Released	2018-06-27
Method	X-RAY DIFFRACTION 2.105 Å
Organisms	Homo sapiens
Macromolecule	THR-LYS-ALA-ALA-ARG-ALY-SER-ALA-PRO-ALA (protein) YEATS domain-containing protein 4 (protein)
Unique Ligands	ACT

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7DN3 \| pdb_00007dn3	Download File View File

Structure of Human RNA Polymerase III elongation complex

Li, L., Yu, Z., Zhao, D., Ren, Y., Hou, H., Xu, Y.

(2021) Cell Res 31: 791-800

Released	2021-03-17
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 17 Unique nucleic acid chains: 3
Unique Ligands	MG, SF4, ZN

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7DU2 \| pdb_00007du2	Download File View File

RNA polymerase III EC complex in post-translocation state

Li, L., Yu, Z., Zhao, D., Ren, Y., Hou, H., Xu, Y.

(2021) Cell Res 31: 791-800

Released	2021-03-17
Method	ELECTRON MICROSCOPY 3.35 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 17 Unique nucleic acid chains: 3
Unique Ligands	MG, SF4, ZN