Author results

4U0M
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STRUCTURE OF THE VIBRIO CHOLERAE DI-NUCLEOTIDE CYCLASE (DNCV) MUTANT D193N IN COMPLEX WITH ATP, GTP AND 5MTHFGLU2
Descriptor:Cyclic AMP-GMP synthase, GUANOSINE-5'-TRIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, ...
Authors:Zhu, D., Xiang, Y.
Deposit date:2014-07-12
Release date:2014-09-17
Last modified:2014-10-22
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural Biochemistry of a Vibrio cholerae Dinucleotide Cyclase Reveals Cyclase Activity Regulation by Folates.
Mol.Cell, 55, 2014
3K49
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PUF3 RNA BINDING DOMAIN BOUND TO COX17 RNA 3' UTR RECOGNITION SEQUENCE SITE B
Descriptor:mRNA-binding protein PUF3, RNA (5'-R(*CP*CP*UP*GP*UP*AP*AP*AP*UP*A)-3'), CITRIC ACID
Authors:Zhu, D., Stumpf, C.R., Krahn, J.M., Wickens, M., Hall, T.M.T.
Deposit date:2009-10-05
Release date:2009-10-27
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs.
Proc.Natl.Acad.Sci.USA, 106, 2009
3K4E
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PUF3 RNA BINDING DOMAIN BOUND TO COX17 RNA 3' UTR RECOGNITION SEQUENCE SITE A
Descriptor:mRNA-binding protein PUF3, RNA (5'-R(P*CP*UP*UP*GP*UP*AP*UP*AP*UP*A)-3')
Authors:Zhu, D., Stumpf, C.R., Krahn, J.M., Wickens, M., Hall, T.M.T.
Deposit date:2009-10-05
Release date:2009-10-27
Last modified:2018-01-24
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs.
Proc.Natl.Acad.Sci.USA, 106, 2009
4F5W
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CRYSTAL STRUCTURE OF LIGAND FREE HUMAN STING CTD
Descriptor:Transmembrane protein 173, CALCIUM ION
Authors:Gu, L., Shang, G., Zhu, D., Li, N., Zhang, J., Zhu, C., Lu, D., Liu, C., Yu, Q., Zhao, Y., Xu, S.
Deposit date:2012-05-13
Release date:2012-06-27
Last modified:2013-09-04
Method:X-RAY DIFFRACTION (2.201 Å)
Cite:Crystal structures of STING protein reveal basis for recognition of cyclic di-GMP
Nat.Struct.Mol.Biol., 19, 2012
4F5Y
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CRYSTAL STRUCTURE OF HUMAN STING CTD COMPLEX WITH C-DI-GMP
Descriptor:Transmembrane protein 173, CALCIUM ION, 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
Authors:Gu, L., Shang, G., Zhu, D., Li, N., Zhang, J., Zhu, C., Lu, D., Liu, C., Yu, Q., Zhao, Y., Xu, S.
Deposit date:2012-05-13
Release date:2012-06-27
Last modified:2013-09-04
Method:X-RAY DIFFRACTION (2.396 Å)
Cite:Crystal structures of STING protein reveal basis for recognition of cyclic di-GMP
Nat.Struct.Mol.Biol., 19, 2012
3TEF
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CRYSTAL STRUCTURE OF THE PERIPLASMIC CATECHOLATE-SIDEROPHORE BINDING PROTEIN VCTP FROM VIBRIO CHOLERAE
Descriptor:Iron(III) ABC transporter, periplasmic iron-compound-binding protein
Authors:Liu, X., Wang, Z., Liu, S., Li, N., Chen, Y., Zhu, C., Zhu, D., Wei, T., Huang, Y., Xu, S., Gu, L.
Deposit date:2011-08-13
Release date:2012-08-15
Method:X-RAY DIFFRACTION (1.698 Å)
Cite:Crystal structure of periplasmic catecholate-siderophore binding protein VctP from Vibrio cholerae at 1.7 A resolution
Febs Lett., 586, 2012
5TIS
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ROOM TEMPERATURE XFEL STRUCTURE OF THE NATIVE, DOUBLY-ILLUMINATED PHOTOSYSTEM II COMPLEX
Descriptor:Photosystem II protein D1 1, Photosystem II CP47 reaction center protein, Photosystem II CP43 reaction center protein, ...
Authors:Young, I.D., Ibrahim, M., Chatterjee, R., Gul, S., Fuller, F., Koroidov, S., Brewster, A.S., Tran, R., Alonso-Mori, R., Kroll, T., Michels-Clark, T., Laksmono, H., Sierra, R.G., Stan, C.A., Hussein, R., Zhang, M., Douthit, L., Kubin, M., de Lichtenberg, C., Pham, L.V., Nilsson, H., Cheah, M.H., Shevela, D., Saracini, C., Bean, M.A., Seuffert, I., Sokaras, D., Weng, T.-C., Pastor, E., Weninger, C., Fransson, T., Lassalle, L., Braeuer, P., Aller, P., Docker, P.T., Andi, B., Orville, A.M., Glownia, J.M., Nelson, S., Sikorski, M., Zhu, D., Hunter, M.S., Aquila, A., Koglin, J.E., Robinson, J., Liang, M., Boutet, S., Lyubimov, A.Y., Uervirojnangkoorn, M., Moriarty, N.W., Liebschner, D., Afonine, P.V., Watermann, D.G., Evans, G., Wernet, P., Dobbek, H., Weis, W.I., Brunger, A.T., Zwart, P.H., Adams, P.D., Zouni, A., Messinger, J., Bergmann, U., Sauter, N.K., Kern, J., Yachandra, V.K., Yano, J.
Deposit date:2016-10-03
Release date:2016-11-23
Last modified:2019-11-20
Method:X-RAY DIFFRACTION (2.250004 Å)
Cite:Structure of photosystem II and substrate binding at room temperature.
Nature, 540, 2016
3SFV
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CRYSTAL STRUCTURE OF THE GDP-BOUND RAB1A S25N MUTANT IN COMPLEX WITH THE COILED-COIL DOMAIN OF LIDA FROM LEGIONELLA PNEUMOPHILA
Descriptor:Ras-related protein Rab-1A, LidA protein, substrate of the Dot/Icm system, ...
Authors:Yin, K., Lu, D., Zhu, D., Zhang, H., Li, B., Xu, S., Gu, L.
Deposit date:2011-06-14
Release date:2012-04-18
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Structural Insights into a Unique Legionella pneumophila Effector LidA Recognizing Both GDP and GTP Bound Rab1 in Their Active State
Plos Pathog., 8, 2012
3SP4
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CRYSTAL STRUCTURE OF APRATAXIN ORTHOLOG HNT3 FROM SCHIZOSACCHAROMYCES POMBE
Descriptor:Aprataxin-like protein, ZINC ION, SULFATE ION
Authors:Gong, Y., Zhu, D., Ding, J., Dou, C., Ren, X., Jiang, T., Wang, D.
Deposit date:2011-07-01
Release date:2011-10-12
Last modified:2013-07-03
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA
Nat.Struct.Mol.Biol., 18, 2011
3SPD
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CRYSTAL STRUCTURE OF APRATAXIN ORTHOLOG HNT3 IN COMPLEX WITH DNA
Descriptor:Aprataxin-like protein, DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3'), DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3'), ...
Authors:Gong, Y., Zhu, D., Ding, J., Dou, C., Ren, X., Jiang, T., Wang, D.
Deposit date:2011-07-01
Release date:2011-10-12
Last modified:2013-07-03
Method:X-RAY DIFFRACTION (1.912 Å)
Cite:Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA
Nat.Struct.Mol.Biol., 18, 2011
3SPL
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CRYSTAL STRUCTURE OF APRATAXIN ORTHOLOG HNT3 IN COMPLEX WITH DNA AND AMP
Descriptor:Aprataxin-like protein, DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3'), DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3'), ...
Authors:Gong, Y., Zhu, D., Ding, J., Dou, C., Ren, X., Jiang, T., Wang, D.
Deposit date:2011-07-02
Release date:2011-10-12
Last modified:2013-07-03
Method:X-RAY DIFFRACTION (2.101 Å)
Cite:Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA
Nat.Struct.Mol.Biol., 18, 2011
3TKL
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CRYSTAL STRUCTURE OF THE GTP-BOUND RAB1A IN COMPLEX WITH THE COILED-COIL DOMAIN OF LIDA FROM LEGIONELLA PNEUMOPHILA
Descriptor:Ras-related protein Rab-1A, LidA protein, substrate of the Dot/Icm system, ...
Authors:Cheng, W., Yin, K., Lu, D., Li, B., Zhu, D., Chen, Y., Zhang, H., Xu, S., Chai, J., Gu, L.
Deposit date:2011-08-27
Release date:2012-06-27
Method:X-RAY DIFFRACTION (2.183 Å)
Cite:Structural insights into a unique Legionella pneumophila effector LidA recognizing both GDP and GTP bound Rab1 in their active state
Plos Pathog., 8, 2012
1FI7
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SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF CYTOCHROME C
Descriptor:CYTOCHROME C, IMIDAZOLE, HEME C
Authors:Banci, L., Bertini, I., Liu, G., Lu, J., Reddig, T., Tang, W., Wu, Y., Zhu, D.
Deposit date:2000-08-03
Release date:2000-08-23
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Effects of extrinsic imidazole ligation on the molecular and electronic structure of cytochrome c
J.Biol.Inorg.Chem., 6, 2001
1FI9
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SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF CYTOCHROME C
Descriptor:CYTOCHROME C, IMIDAZOLE, HEME C
Authors:Banci, L., Bertini, I., Liu, G., Lu, J., Reddig, T., Tang, W., Wu, Y., Zhu, D.
Deposit date:2000-08-03
Release date:2000-08-23
Last modified:2011-07-13
Method:SOLUTION NMR
Cite:Effects of extrinsic imidazole ligation on the molecular and electronic structure of cytochrome c
J.Biol.Inorg.Chem., 6, 2001
3O72
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CRYSTAL STRUCTURE OF EFEB IN COMPLEX WITH HEME
Descriptor:Redox component of a tripartite ferrous iron transporter, PROTOPORPHYRIN IX CONTAINING FE, OXYGEN MOLECULE
Authors:Liu, X., Du, Q., Wang, Z., Zhu, D., Huang, Y., Li, N., Xu, S., Gu, L.
Deposit date:2010-07-30
Release date:2011-03-16
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Crystal structure and biochemical features of EfeB/YcdB from Escherichia coli O157: ASP235 plays divergent roles in different enzyme-catalyzed processes
J.Biol.Chem., 286, 2011
3Q7J
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ENGINEERED THERMOPLASMA ACIDOPHILUM F3 FACTOR MIMICS HUMAN AMINOPEPTIDASE N (APN) AS A TARGET FOR ANTICANCER DRUG DEVELOPMENT
Descriptor:Tricorn protease-interacting factor F3, ZINC ION, L-phenylalanyl-N6-[(benzyloxy)carbonyl]-N1-hydroxy-L-lysinamide
Authors:Su, J., Wang, Q., Feng, J., Zhang, C., Zhu, D., We, T., Xu, W., Gu, L.
Deposit date:2011-01-05
Release date:2011-07-27
Method:X-RAY DIFFRACTION (2.91 Å)
Cite:Engineered Thermoplasma acidophilum factor F3 mimics human aminopeptidase N (APN) as a target for anticancer drug development
Bioorg.Med.Chem., 19, 2011
3TB4
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CRYSTAL STRUCTURE OF THE ISC DOMAIN OF VIBB
Descriptor:Vibriobactin-specific isochorismatase, B-OCTYLGLUCOSIDE, TRIETHYLENE GLYCOL, ...
Authors:Liu, S., Zhang, C., Niu, B., Li, N., Liu, M., Wei, T., Zhu, D., Xu, S., Gu, L.
Deposit date:2011-08-05
Release date:2012-08-29
Last modified:2014-01-01
Method:X-RAY DIFFRACTION (1.35 Å)
Cite:Structural insight into the ISC domain of VibB from Vibrio cholerae at atomic resolution: a snapshot just before the enzymatic reaction
Acta Crystallogr.,Sect.D, 68, 2012
3TG2
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CRYSTAL STRUCTURE OF THE ISC DOMAIN OF VIBB IN COMPLEX WITH ISOCHORISMATE
Descriptor:Vibriobactin-specific isochorismatase, (5S,6S)-5-[(1-carboxyethenyl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylic acid, TRIETHYLENE GLYCOL
Authors:Liu, S., Zhang, C., Niu, B., Li, N., Liu, X., Liu, M., Wei, T., Zhu, D., Huang, Y., Xu, S., Gu, L.
Deposit date:2011-08-17
Release date:2012-08-29
Last modified:2014-01-01
Method:X-RAY DIFFRACTION (1.101 Å)
Cite:Structural insight into the ISC domain of VibB from Vibrio cholerae at atomic resolution: a snapshot just before the enzymatic reaction
Acta Crystallogr.,Sect.D, 68, 2012
3TGV
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CRYSTAL STRUCTURE OF HUTZ,THE HEME STORSGE PROTEIN FROM VIBRIO CHOLERAE
Descriptor:Heme-binding protein HutZ, BENZOIC ACID
Authors:Liu, X., Gong, J., Wang, Z., Du, Q., Wei, T., Zhu, D., Huang, Y., Xu, S., Gu, L.
Deposit date:2011-08-17
Release date:2012-08-22
Method:X-RAY DIFFRACTION (1.999 Å)
Cite:Crystal structure of HutZ,the heme storsge protein from Vibrio cholerae
To be Published
3TLQ
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CRYSTAL STRUCTURE OF EAL-LIKE DOMAIN PROTEIN YDIV
Descriptor:Regulatory protein YdiV, PHOSPHATE ION, GLYCEROL
Authors:Li, B., Li, N., Wang, F., Guo, L., Liu, C., Zhu, D., Xu, S., Gu, L.
Deposit date:2011-08-30
Release date:2012-09-12
Last modified:2013-07-03
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility
Nucleic Acids Res., 40, 2012
4DOY
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CRYSTAL STRUCTURE OF DIBENZOTHIOPHENE DESULFURIZATION ENZYME C
Descriptor:Dibenzothiophene desulfurization enzyme C, GLYCEROL
Authors:Liu, S., Zhang, C., Zhu, D., Gu, L.
Deposit date:2012-02-12
Release date:2013-02-13
Last modified:2014-12-24
Method:X-RAY DIFFRACTION (1.789 Å)
Cite:Crystal structure of DszC from Rhodococcus sp. XP at 1.79 angstrom
Proteins, 82, 2014
4GO3
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CRYSTAL STRUCTURE OF PNPE FROM PSEUDOMONAS SP. WBC-3
Descriptor:Putative gamma-hydroxymuconic semialdehyde dehydrogenase
Authors:Su, J., Zhang, C., Liu, S., Zhu, D., Gu, L.
Deposit date:2012-08-18
Release date:2014-02-26
Method:X-RAY DIFFRACTION (2.704 Å)
Cite:Crystal structure of PnpE from Pseudomonas sp. WBC-3
To be Published
4GO4
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CRYSTAL STRUCTURE OF PNPE IN COMPLEX WITH NICOTINAMIDE ADENINE DINUCLEOTIDE
Descriptor:Putative gamma-hydroxymuconic semialdehyde dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Authors:Su, J., Zhang, C., Liu, S., Zhu, D., Gu, L.
Deposit date:2012-08-18
Release date:2013-09-04
Method:X-RAY DIFFRACTION (3.099 Å)
Cite:Crystal structure of PnpE in complex with Nicotinamide adenine dinucleotide
To be Published
4RL0
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STRUCTURAL AND MECHANISTIC INSIGHTS INTO NDM-1 CATALYZED HYDROLYSIS OF CEPHALOSPORINS
Descriptor:Beta-lactamase NDM-1, ZINC ION, (2R,5S)-5-[(carbamoyloxy)methyl]-2-[(R)-carboxy{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}methyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
Authors:Feng, H., Ding, J., Zhu, D., Liu, X., Xu, X., Zhang, Y., Zang, S., Wang, D.-C., Liu, W.
Deposit date:2014-10-14
Release date:2014-11-19
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:Structural and Mechanistic Insights into NDM-1 Catalyzed Hydrolysis of Cephalosporins.
J.Am.Chem.Soc., 136, 2014
4RL2
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STRUCTURAL AND MECHANISTIC INSIGHTS INTO NDM-1 CATALYZED HYDROLYSIS OF CEPHALOSPORINS
Descriptor:Beta-lactamase NDM-1, ZINC ION, (1R)-2-({(R)-carboxy[(2R,5S)-4-carboxy-5-methyl-5,6-dihydro-2H-1,3-thiazin-2-yl]methyl}amino)-2-oxo-1-phenylethanaminium
Authors:Feng, H., Ding, J., Zhu, D., Liu, X., Xu, X., Zhang, Y., Zang, S., Wang, D.-C., Liu, W.
Deposit date:2014-10-15
Release date:2014-11-19
Method:X-RAY DIFFRACTION (2.008 Å)
Cite:Structural and Mechanistic Insights into NDM-1 Catalyzed Hydrolysis of Cephalosporins.
J.Am.Chem.Soc., 136, 2014