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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Zhu, D."

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Search Summary

This query matches 34 Structures.

Refinements

Structure Determination Methodology

experimental (34)

Scientific Name of Source Organism

	Homo sapiens (4)
	Klebsiella pneumoniae (4)
	Gallus gallus (3)
	Schizosaccharomyces pombe 972h- (3)
	Vibrio cholerae (3)
	Equus caballus (2)
	Legionella pneumophila str. Corby (2)
	Pseudomonas sp. WBC-3 (2)
	Saccharomyces cerevisiae (2)
	Escherichia coli K-12 (1)

More...

Taxonomy

	Bacteria (21)
	Eukaryota (14)
	Archaea (1)

Experimental Method

	X-RAY DIFFRACTION (32)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (34)
	DNA (2)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (8)
	2.0 - 2.5 (13)
	2.5 - 3.0 (6)
	3.0 - 3.5 (2)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (2)
	2010 - 2014 (21)
	2015 - 2019 (6)
	2020 - 2024 (3)

Enzyme Classification Name

	Hydrolases (14)
	Oxidoreductases (5)
	Transferases (1)
	Lyases (1)

Membrane Protein Annotation

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

Symmetry Type

	Asymmetric (19)
	Cyclic (18)

SCOP Classification

	Membrane and cell surface proteins and peptides (1)
	Alpha and beta proteins (a+b) (8)
	All alpha proteins (5)
	Artifacts (2)
	All beta proteins (2)
	Alpha and beta proteins (a/b) (5)

AllSelected

1 to 25 of 34 Structures

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1FI7 \| pdb_00001fi7	Download File View File

Solution structure of the imidazole complex of cytochrome C

Banci, L., Bertini, I., Liu, G., Lu, J., Reddig, T., Tang, W., Wu, Y., Zhu, D.

(2001) J Biol Inorg Chem 6: 628-637

Released	2000-08-23
Method	SOLUTION NMR
Organisms	Equus caballus
Macromolecule	CYTOCHROME C (protein)
Unique Ligands	HEC, IMD

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1FI9 \| pdb_00001fi9	Download File View File

SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF CYTOCHROME C

Banci, L., Bertini, I., Liu, G., Lu, J., Reddig, T., Tang, W., Wu, Y., Zhu, D.

(2001) J Biol Inorg Chem 6: 628-637

Released	2000-08-23
Method	SOLUTION NMR
Organisms	Equus caballus
Macromolecule	CYTOCHROME C (protein)
Unique Ligands	HEC, IMD

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3K49 \| pdb_00003k49	Download File View File

Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site B

Zhu, D., Stumpf, C.R., Krahn, J.M., Wickens, M., Hall, T.M.T.

(2009) Proc Natl Acad Sci U S A 106: 20192-20197

Released	2009-10-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	mRNA-binding protein PUF3 (protein) RNA (5'-R(CPCPUPGPUPAPAPAPUPA)-3') (nucleic acid)
Unique Ligands	CIT

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3K4E \| pdb_00003k4e	Download File View File

Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site A

Zhu, D., Stumpf, C.R., Krahn, J.M., Wickens, M., Hall, T.M.T.

(2009) Proc Natl Acad Sci U S A 106: 20192-20197

Released	2009-10-27
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	mRNA-binding protein PUF3 (protein) RNA (5'-R(PCPUPUPGPUPAPUPAPUPA)-3') (nucleic acid)

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3O72 \| pdb_00003o72	Download File View File

Crystal structure of EfeB in complex with heme

Liu, X., Du, Q., Wang, Z., Zhu, D., Huang, Y., Li, N., Xu, S., Gu, L.

(2011) J Biological Chem 286: 14922-14931

Released	2011-03-16
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Escherichia coli O157:H7 str. TW14359
Macromolecule	Redox component of a tripartite ferrous iron transporter (protein)
Unique Ligands	HEM, OXY

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3Q7J \| pdb_00003q7j	Download File View File

Engineered Thermoplasma Acidophilum F3 factor mimics human aminopeptidase N (APN) as a target for anticancer drug development

Su, J., Wang, Q., Feng, J., Zhang, C., Zhu, D., We, T., Xu, W., Gu, L.

(2011) Bioorg Med Chem 19: 2991-2996

Released	2011-07-27
Method	X-RAY DIFFRACTION 2.91 Å
Organisms	Thermoplasma acidophilum DSM 1728
Macromolecule	Tricorn protease-interacting factor F3 (protein)
Unique Ligands	FBO, ZN

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3SFV \| pdb_00003sfv	Download File View File

Crystal structure of the GDP-bound Rab1a S25N mutant in complex with the coiled-coil domain of LidA from Legionella pneumophila

Yin, K., Lu, D., Zhu, D., Zhang, H., Li, B., Xu, S., Gu, L.

(2012) PLoS Pathog 8: e1002528-e1002528

Released	2012-04-18
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Homo sapiens Legionella pneumophila str. Corby
Macromolecule	LidA protein, substrate of the Dot/Icm system (protein) Ras-related protein Rab-1A (protein)
Unique Ligands	GDP

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3SP4 \| pdb_00003sp4	Download File View File

Crystal structure of aprataxin ortholog Hnt3 from Schizosaccharomyces pombe

Gong, Y., Zhu, D., Ding, J., Dou, C., Ren, X., Jiang, T., Wang, D.

(2011) Nat Struct Mol Biol 18: 1297-1299

Released	2011-10-12
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Aprataxin-like protein (protein)
Unique Ligands	SO4, ZN

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3SPD \| pdb_00003spd	Download File View File

Crystal structure of aprataxin ortholog Hnt3 in complex with DNA

Gong, Y., Zhu, D., Ding, J., Dou, C., Ren, X., Jiang, T., Wang, D.

(2011) Nat Struct Mol Biol 18: 1297-1299

Released	2011-10-12
Method	X-RAY DIFFRACTION 1.912 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Aprataxin-like protein (protein) DNA (5'-D(GPTPCPAPCPTPAPTPCPGPGPAPAPTPGPAPG)-3') (nucleic acid) DNA (5'-D(TPAPTPTPCPCPGPAPTPAPGPTPGPAPC)-3') (nucleic acid)
Unique Ligands	SO4, ZN

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3SPL \| pdb_00003spl	Download File View File

Crystal structure of aprataxin ortholog Hnt3 in complex with DNA and AMP

Gong, Y., Zhu, D., Ding, J., Dou, C., Ren, X., Jiang, T., Wang, D.

(2011) Nat Struct Mol Biol 18: 1297-1299

Released	2011-10-12
Method	X-RAY DIFFRACTION 2.101 Å
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Aprataxin-like protein (protein) DNA (5'-D(GPTPCPAPCPTPAPTPCPGPGPAPAPTPGPAPG)-3') (nucleic acid) DNA (5'-D(TPAPTPTPCPCPGPAPTPAPGPTPGPAPC)-3') (nucleic acid)
Unique Ligands	AMP, SO4, ZN

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3TB4 \| pdb_00003tb4	Download File View File

Crystal structure of the ISC domain of VibB

Liu, S., Zhang, C., Niu, B., Li, N., Liu, M., Wei, T., Zhu, D., Xu, S., Gu, L.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1329-1338

Released	2012-08-29
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Vibrio cholerae
Macromolecule	Vibriobactin-specific isochorismatase (protein)
Unique Ligands	BOG, CA, EDO, PEG, PGE

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3TEF \| pdb_00003tef	Download File View File

Crystal Structure of the Periplasmic Catecholate-Siderophore Binding Protein VctP from Vibrio Cholerae

Liu, X., Wang, Z., Liu, S., Li, N., Chen, Y., Zhu, C., Zhu, D., Wei, T., Huang, Y., Xu, S., Gu, L.

(2012) FEBS Lett 586: 1240-1244

Released	2012-08-15
Method	X-RAY DIFFRACTION 1.698 Å
Organisms	Vibrio cholerae
Macromolecule	Iron(III) ABC transporter, periplasmic iron-compound-binding protein (protein)

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3TG2 \| pdb_00003tg2	Download File View File

Crystal structure of the ISC domain of VibB in complex with isochorismate

Liu, S., Zhang, C., Niu, B., Li, N., Liu, X., Liu, M., Wei, T., Zhu, D., Huang, Y., Xu, S., Gu, L.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1329-1338

Released	2012-08-29
Method	X-RAY DIFFRACTION 1.101 Å
Organisms	Vibrio cholerae
Macromolecule	Vibriobactin-specific isochorismatase (protein)
Unique Ligands	ISC, PGE

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3TGV \| pdb_00003tgv	Download File View File

Crystal structure of HutZ,the heme storsge protein from Vibrio cholerae

Liu, X., Gong, J., Wang, Z., Du, Q., Wei, T., Zhu, D., Huang, Y., Xu, S., Gu, L.

To be published

Released	2012-08-22
Method	X-RAY DIFFRACTION 1.999 Å
Organisms	Vibrio cholerae O395
Macromolecule	Heme-binding protein HutZ (protein)
Unique Ligands	BEZ

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3TKL \| pdb_00003tkl	Download File View File

Crystal structure of the GTP-bound Rab1a in complex with the coiled-coil domain of LidA from Legionella pneumophila

Cheng, W., Yin, K., Lu, D., Li, B., Zhu, D., Chen, Y., Zhang, H., Xu, S., Chai, J., Gu, L.

(2012) PLoS Pathog 8: e1002528-e1002528

Released	2012-06-27
Method	X-RAY DIFFRACTION 2.183 Å
Organisms	Homo sapiens Legionella pneumophila str. Corby
Macromolecule	LidA protein, substrate of the Dot/Icm system (protein) Ras-related protein Rab-1A (protein)
Unique Ligands	GTP, MG

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3TLQ \| pdb_00003tlq	Download File View File

Crystal structure of EAL-like domain protein YdiV

Li, B., Li, N., Wang, F., Guo, L., Liu, C., Zhu, D., Xu, S., Gu, L.

(2012) Nucleic Acids Res 40: 11073-11085

Released	2012-09-12
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Escherichia coli K-12
Macromolecule	Regulatory protein YdiV (protein)
Unique Ligands	GOL, PO4

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4DOY \| pdb_00004doy	Download File View File

Crystal structure of Dibenzothiophene desulfurization enzyme C

Liu, S., Zhang, C., Zhu, D., Gu, L.

(2014) Proteins 82: 1708-1720

Released	2013-02-13
Method	X-RAY DIFFRACTION 1.789 Å
Organisms	Rhodococcus erythropolis XP
Macromolecule	Dibenzothiophene desulfurization enzyme C (protein)
Unique Ligands	GOL

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4F5W \| pdb_00004f5w	Download File View File

Crystal structure of ligand free human STING CTD

Gu, L., Shang, G., Zhu, D., Li, N., Zhang, J., Zhu, C., Lu, D., Liu, C., Yu, Q., Zhao, Y., Xu, S.

(2012) Nat Struct Mol Biol 19: 725-727

Released	2012-06-27
Method	X-RAY DIFFRACTION 2.201 Å
Organisms	Homo sapiens
Macromolecule	Transmembrane protein 173 (protein)
Unique Ligands	CA

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4F5Y \| pdb_00004f5y	Download File View File

Crystal structure of human STING CTD complex with C-di-GMP

Gu, L., Shang, G., Zhu, D., Li, N., Zhang, J., Zhu, C., Lu, D., Liu, C., Yu, Q., Zhao, Y., Xu, S.

(2012) Nat Struct Mol Biol 19: 725-727

Released	2012-06-27
Method	X-RAY DIFFRACTION 2.396 Å
Organisms	Homo sapiens
Macromolecule	Transmembrane protein 173 (protein)
Unique Ligands	C2E, CA

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4GO3 \| pdb_00004go3	Download File View File

Crystal structure of PnpE from Pseudomonas sp. WBC-3

Su, J., Zhang, C., Liu, S., Zhu, D., Gu, L.

To be published

Released	2014-02-26
Method	X-RAY DIFFRACTION 2.704 Å
Organisms	Pseudomonas sp. WBC-3
Macromolecule	Putative gamma-hydroxymuconic semialdehyde dehydrogenase (protein)

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4GO4 \| pdb_00004go4	Download File View File

Crystal structure of PnpE in complex with Nicotinamide adenine dinucleotide

Su, J., Zhang, C., Liu, S., Zhu, D., Gu, L.

To be published

Released	2013-09-04
Method	X-RAY DIFFRACTION 3.099 Å
Organisms	Pseudomonas sp. WBC-3
Macromolecule	Putative gamma-hydroxymuconic semialdehyde dehydrogenase (protein)
Unique Ligands	NAD

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4RL0 \| pdb_00004rl0	Download File View File

Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins

Feng, H., Ding, J., Zhu, D., Liu, X., Xu, X., Zhang, Y., Zang, S., Wang, D.-C., Liu, W.

(2014) J Am Chem Soc 136: 14694-14697

Released	2014-11-19
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase NDM-1 (protein)
Unique Ligands	3S0, ZN

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4RL2 \| pdb_00004rl2	Download File View File

Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins

Feng, H., Ding, J., Zhu, D., Liu, X., Xu, X., Zhang, Y., Zang, S., Wang, D.-C., Liu, W.

(2014) J Am Chem Soc 136: 14694-14697

Released	2014-11-19
Method	X-RAY DIFFRACTION 2.008 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase NDM-1 (protein)
Unique Ligands	3S3, ZN

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4RM5 \| pdb_00004rm5	Download File View File

Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins

Feng, H., Ding, J., Zhu, D., Liu, X., Xu, X., Zhang, Y., Zang, S., Wang, D.-C., Liu, W.

(2014) J Am Chem Soc 136: 14694-14697

Released	2014-11-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase NDM-1 (protein)
Unique Ligands	ZN

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4U0M \| pdb_00004u0m	Download File View File

Structure of the Vibrio cholerae di-nucleotide cyclase (DncV) mutant D193N in complex with ATP, GTP and 5MTHFGLU2

Zhu, D., Xiang, Y.

(2014) Mol Cell 55: 931-937

Released	2014-09-17
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Vibrio cholerae O1 biovar El Tor str. N16961
Macromolecule	Cyclic AMP-GMP synthase (protein)
Unique Ligands	ATP, GTP, MG, TLL

1 to 25 of 34 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

1FI7 | pdb_00001fi7

1FI9 | pdb_00001fi9

3K49 | pdb_00003k49

3K4E | pdb_00003k4e

3O72 | pdb_00003o72

3Q7J | pdb_00003q7j

3SFV | pdb_00003sfv

3SP4 | pdb_00003sp4

3SPD | pdb_00003spd

3SPL | pdb_00003spl

3TB4 | pdb_00003tb4

3TEF | pdb_00003tef

3TG2 | pdb_00003tg2

3TGV | pdb_00003tgv

3TKL | pdb_00003tkl

3TLQ | pdb_00003tlq

4DOY | pdb_00004doy

4F5W | pdb_00004f5w

4F5Y | pdb_00004f5y

4GO3 | pdb_00004go3

4GO4 | pdb_00004go4

4RL0 | pdb_00004rl0

4RL2 | pdb_00004rl2

4RM5 | pdb_00004rm5

4U0M | pdb_00004u0m