4MDF
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4mdf by Molmil](/molmil-images/mine/4mdf) | Structure of bacterial polynucleotide kinase Michaelis complex bound to GTP and DNA | Descriptor: | CITRIC ACID, DNA (5'-D(*CP*CP*TP*GP*T)-3'), GUANOSINE-5'-TRIPHOSPHATE, ... | Authors: | Shuman, S, Das, U, Wang, L.K, Smith, P, Jacewicz, A. | Deposit date: | 2013-08-22 | Release date: | 2013-11-06 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.727 Å) | Cite: | Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP*Mg2+ and 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition. Nucleic Acids Res., 42, 2014
|
|
4MDE
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4mde by Molmil](/molmil-images/mine/4mde) | Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA | Descriptor: | DNA (5'-D(P*CP*CP*TP*GP*T)-3'), GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | Authors: | Shuman, S, Das, U, Wang, L.K, Smith, P, Jacewicz, A. | Deposit date: | 2013-08-22 | Release date: | 2013-11-06 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP*Mg2+ and 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition. Nucleic Acids Res., 42, 2014
|
|
7T6D
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7t6d by Molmil](/molmil-images/mine/7t6d) | CryoEM structure of the YejM/LapB complex | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE, Inner membrane protein YejM, ... | Authors: | Mi, W, Shu, S. | Deposit date: | 2021-12-13 | Release date: | 2022-08-17 | Last modified: | 2024-02-28 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli. Nat Commun, 13, 2022
|
|
8V24
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 8v24 by Molmil](/molmil-images/mine/8v24) | LapB cytoplasmic domain in complex with LpxC | Descriptor: | ACETATE ION, Lipopolysaccharide assembly protein B, UDP-3-O-acyl-N-acetylglucosamine deacetylase, ... | Authors: | Mi, W, Shu, S. | Deposit date: | 2023-11-21 | Release date: | 2024-04-24 | Last modified: | 2024-05-08 | Method: | ELECTRON MICROSCOPY (3.6 Å) | Cite: | Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis. Proc.Natl.Acad.Sci.USA, 121, 2024
|
|
5TC1
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5tc1 by Molmil](/molmil-images/mine/5tc1) | In situ structures of the genome and genome-delivery apparatus in ssRNA bacteriophage MS2 | Descriptor: | Capsid protein, Maturation protein, phage MS2 genome | Authors: | Dai, X.H, Li, Z.H, Lai, M, Shu, S, Du, Y.S, Zhou, Z.H, Sun, R. | Deposit date: | 2016-09-13 | Release date: | 2016-12-07 | Last modified: | 2018-07-18 | Method: | ELECTRON MICROSCOPY (3.6 Å) | Cite: | In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus. Nature, 541, 2017
|
|
6M8Z
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6m8z by Molmil](/molmil-images/mine/6m8z) | Crystal structure of human DJ-1 without a modification on Cys-106 | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CHLORIDE ION, Protein/nucleic acid deglycase DJ-1 | Authors: | Shumilin, I.A, Shabalin, I.G, Shumilina, S.V, Werenskjold, C, Utepbergenov, D, Minor, W. | Deposit date: | 2018-08-22 | Release date: | 2018-09-05 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.83 Å) | Cite: | A transient post-translational modification of active site cysteine alters binding properties of the parkinsonism protein DJ-1. Biochem. Biophys. Res. Commun., 504, 2018
|
|
1MQQ
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1mqq by Molmil](/molmil-images/mine/1mqq) | THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE FROM BACILLUS STEAROTHERMOPHILUS T-1 COMPLEXED WITH GLUCURONIC ACID | Descriptor: | ALPHA-D-GLUCURONIDASE, GLYCEROL, alpha-D-glucopyranuronic acid | Authors: | Golan, G, Shallom, D, Teplitsky, A, Zaide, G, Shulami, S, Baasov, T, Stojanoff, V, Thompson, A, Shoham, Y, Shoham, G. | Deposit date: | 2002-09-17 | Release date: | 2003-09-17 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications. J.Biol.Chem., 279, 2004
|
|
3VV6
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3vv6 by Molmil](/molmil-images/mine/3vv6) | Crystal Structure of beta secetase in complex with 2-amino-3-methyl-6-((1S, 2R)-2-phenylcyclopropyl)pyrimidin-4(3H)-one | Descriptor: | 2-amino-3-methyl-6-[(1S,2R)-2-phenylcyclopropyl]pyrimidin-4(3H)-one, Beta-secretase 1, GLYCEROL, ... | Authors: | Yonezawa, S, Yamamoto, T, Yamakawa, H, Muto, C, Hosono, M, Hattori, K, Higashino, K, Sakagami, M, Togame, H, Tanaka, Y, Nakano, T, Takemoto, H, Arisawa, M, Shuto, S. | Deposit date: | 2012-07-17 | Release date: | 2012-10-24 | Last modified: | 2017-11-22 | Method: | X-RAY DIFFRACTION (2.05 Å) | Cite: | Conformational restriction approach to beta-secretase (BACE1) inhibitors: effect of a cyclopropane ring to induce an alternative binding mode J.Med.Chem., 55, 2012
|
|
4WAN
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4wan by Molmil](/molmil-images/mine/4wan) | Crystal structure of Msl5 protein in complex with RNA at 1.8 A | Descriptor: | ACETATE ION, Branchpoint-bridging protein, GLYCEROL, ... | Authors: | Jacewicz, A, Smith, P, Chico, L, Schwer, B, Shuman, S. | Deposit date: | 2014-08-29 | Release date: | 2014-12-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs. Rna, 21, 2015
|
|
4WAL
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4wal by Molmil](/molmil-images/mine/4wal) | Crystal structure of selenomethionine Msl5 protein in complex with RNA at 2.2 A | Descriptor: | Branchpoint-bridging protein, CHLORIDE ION, GLYCEROL, ... | Authors: | Jacewicz, A, Smith, P, Chico, L, Schwer, B, Shuman, S. | Deposit date: | 2014-08-29 | Release date: | 2014-12-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs. Rna, 21, 2015
|
|
4W7S
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4w7s by Molmil](/molmil-images/mine/4w7s) | Crystal structure of the yeast DEAD-box splicing factor Prp28 at 2.54 Angstroms resolution | Descriptor: | GLYCEROL, HEXAETHYLENE GLYCOL, MAGNESIUM ION, ... | Authors: | Jacewicz, A, Smith, P, Schwer, B, Shuman, S. | Deposit date: | 2014-08-22 | Release date: | 2014-10-29 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.542 Å) | Cite: | Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28. Nucleic Acids Res., 42, 2014
|
|
7SJR
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7sjr by Molmil](/molmil-images/mine/7sjr) | Cryo-EM structure of AdnA-AdnB(W325A) in complex with DNA and AMPPNP | Descriptor: | DNA (70-MER), DNA helicase, IRON/SULFUR CLUSTER, ... | Authors: | Wang, J, Warren, G.M, Shuman, S, Patel, D.J. | Deposit date: | 2021-10-18 | Release date: | 2021-12-22 | Last modified: | 2024-06-05 | Method: | ELECTRON MICROSCOPY (3.8 Å) | Cite: | Structure-activity relationships at a nucleobase-stacking tryptophan required for chemomechanical coupling in the DNA resecting motor-nuclease AdnAB. Nucleic Acids Res., 50, 2022
|
|
1MQR
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1mqr by Molmil](/molmil-images/mine/1mqr) | THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE (E386Q) FROM BACILLUS STEAROTHERMOPHILUS T-6 | Descriptor: | ALPHA-D-GLUCURONIDASE, GLYCEROL | Authors: | Golan, G, Shallom, D, Teplitsky, A, Zaide, G, Shulami, S, Baasov, T, Stojanoff, V, Thompson, A, Shoham, Y, Shoham, G. | Deposit date: | 2002-09-17 | Release date: | 2003-09-17 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal Structures of Geobacillus stearothermophilus {alpha}-Glucuronidase Complexed with Its Substrate and Products: MECHANISTIC IMPLICATIONS. J.Biol.Chem., 279, 2004
|
|
1MQP
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 1mqp by Molmil](/molmil-images/mine/1mqp) | THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE FROM BACILLUS STEAROTHERMOPHILUS T-6 | Descriptor: | GLYCEROL, alpha-D-glucuronidase | Authors: | Golan, G, Shallom, D, Teplitsky, A, Zaide, G, Shulami, S, Baasov, T, Stojanoff, V, Thompson, A, Shoham, Y, Shoham, G. | Deposit date: | 2002-09-17 | Release date: | 2003-09-23 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications. J.Biol.Chem., 279, 2004
|
|
6DTR
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6dtr by Molmil](/molmil-images/mine/6dtr) | Apo T. maritima MalE3 | Descriptor: | SULFATE ION, maltose-binding protein MalE3 | Authors: | Cuneo, M.J, Shukla, S. | Deposit date: | 2018-06-18 | Release date: | 2018-09-19 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.301 Å) | Cite: | Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry, 57, 2018
|
|
6DTT
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6dtt by Molmil](/molmil-images/mine/6dtt) | Apo T. maritima MalE2 | Descriptor: | maltose-binding protein MalE2 | Authors: | Cuneo, M.J, Shukla, S. | Deposit date: | 2018-06-18 | Release date: | 2018-09-19 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry, 57, 2018
|
|
6DTS
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6dts by Molmil](/molmil-images/mine/6dts) | Maltotetraose bound T. maritima MalE2 | Descriptor: | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, maltose-binding protein MalE2 | Authors: | Cuneo, M.J, Shukla, S. | Deposit date: | 2018-06-18 | Release date: | 2018-09-19 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry, 57, 2018
|
|
6DTU
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6dtu by Molmil](/molmil-images/mine/6dtu) | Maltotetraose bound T. maritima MalE1 | Descriptor: | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, maltose-binding protein MalE1 | Authors: | Cuneo, M.J, Shukla, S. | Deposit date: | 2018-06-18 | Release date: | 2018-09-19 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry, 57, 2018
|
|
6E33
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6e33 by Molmil](/molmil-images/mine/6e33) | Crystal Structure of Pho7-DNA complex | Descriptor: | DNA (5'-D(*GP*AP*TP*TP*TP*GP*AP*AP*TP*GP*TP*CP*CP*GP*AP*AP*GP*GP*AP*T)-3'), DNA (5'-D(*TP*CP*CP*TP*TP*CP*GP*GP*AP*CP*AP*TP*TP*CP*AP*AP*AP*TP*CP*A)-3'), Uncharacterized transcriptional regulatory protein C27B12.11c, ... | Authors: | Garg, A, Goldgur, Y, Shuman, S. | Deposit date: | 2018-07-13 | Release date: | 2018-10-24 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.705 Å) | Cite: | Distinctive structural basis for DNA recognition by the fission yeast Zn2Cys6 transcription factor Pho7 and its role in phosphate homeostasis. Nucleic Acids Res., 46, 2018
|
|
3M4A
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3m4a by Molmil](/molmil-images/mine/3m4a) | Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site | Descriptor: | ACETIC ACID, DNA (5'-D(*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*CP*GP*CP*CP*CP*TP*TP*AP*TP*TP*C)-3'), ... | Authors: | Patel, A, Yakovleva, L, Shuman, S, Mondragon, A. | Deposit date: | 2010-03-10 | Release date: | 2010-07-14 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site. Structure, 18, 2010
|
|
4GP6
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4gp6 by Molmil](/molmil-images/mine/4gp6) | Polynucleotide kinase | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, Metallophosphoesterase | Authors: | Wang, L.K, Das, U, Smith, P, Shuman, S. | Deposit date: | 2012-08-20 | Release date: | 2012-11-14 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system. Rna, 18, 2012
|
|
4GP7
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4gp7 by Molmil](/molmil-images/mine/4gp7) | Polynucleotide kinase | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, CITRIC ACID, MAGNESIUM ION, ... | Authors: | Wang, L.K, Das, U, Smith, P, Shuman, S. | Deposit date: | 2012-08-20 | Release date: | 2012-11-14 | Last modified: | 2017-11-15 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system. Rna, 18, 2012
|
|
6E5Z
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6e5z by Molmil](/molmil-images/mine/6e5z) | |
8TG3
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 8tg3 by Molmil](/molmil-images/mine/8tg3) | tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with ADP-ribose-1" -phosphate | Descriptor: | DI(HYDROXYETHYL)ETHER, GLYCEROL, NITRATE ION, ... | Authors: | Jacewicz, A, Dantuluri, S, Shuman, S. | Deposit date: | 2023-07-12 | Release date: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.47 Å) | Cite: | Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD. Proc.Natl.Acad.Sci.USA, 120, 2023
|
|
8TG5
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 8tg5 by Molmil](/molmil-images/mine/8tg5) | tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with branched 2'-PO4 RNA | Descriptor: | (2S,3R,4R,5S)-2-(6-amino-9H-purin-9-yl)-4-{[(S)-{[(2R,3S,4R,5S)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-({[(S)-{[(2R,3R,4S,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}(hydroxy)phosphoryl]oxy}methyl)oxolan-3-yl dihydrogen phosphate (non-preferred name), CHLORIDE ION, POTASSIUM ION, ... | Authors: | Jacewicz, A, Dantuluri, S, Shuman, S. | Deposit date: | 2023-07-12 | Release date: | 2024-06-05 | Last modified: | 2024-06-26 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD. Proc.Natl.Acad.Sci.USA, 120, 2023
|
|