5K36
| Structure of an eleven component nuclear RNA exosome complex bound to RNA | Descriptor: | Exosome complex component CSL4, Exosome complex component MTR3, Exosome complex component RRP4, ... | Authors: | Lima, C.D, Zinder, J.C. | Deposit date: | 2016-05-19 | Release date: | 2016-11-02 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3. Mol.Cell, 64, 2016
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3II4
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3I2D
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6U75
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4OO1
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4PN0
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4PN1
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5E6J
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4M52
| Structure of Mtb Lpd bound to SL827 | Descriptor: | Dihydrolipoyl dehydrogenase, FLAVIN-ADENINE DINUCLEOTIDE, N~2~-[(2-amino-5-bromopyridin-3-yl)sulfonyl]-N-(4-methoxyphenyl)-N~2~-methylglycinamide | Authors: | Lima, C.D. | Deposit date: | 2013-08-07 | Release date: | 2013-11-27 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Lipoamide channel-binding sulfonamides selectively inhibit mycobacterial lipoamide dehydrogenase. Biochemistry, 52, 2013
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2NN6
| Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40 | Descriptor: | 3'-5' exoribonuclease CSL4 homolog, Exosome complex exonuclease RRP4, Exosome complex exonuclease RRP40, ... | Authors: | Lima, C.D. | Deposit date: | 2006-10-23 | Release date: | 2006-12-26 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (3.35 Å) | Cite: | Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell(Cambridge,Mass.), 127, 2006
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2Q2T
| Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick | Descriptor: | 5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3', 5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3', 5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3', ... | Authors: | Lima, C.D, Nandakumar, J, Nair, P.A, Smith, P, Shuman, S. | Deposit date: | 2007-05-29 | Release date: | 2007-07-10 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural basis for nick recognition by a minimal pluripotent DNA ligase. Nat.Struct.Mol.Biol., 14, 2007
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2Q2U
| Structure of Chlorella virus DNA ligase-product DNA complex | Descriptor: | 5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3', 5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3', Chlorella virus DNA ligase | Authors: | Lima, C.D, Nandakumar, J, Nair, P.A, Smith, P, Shuman, S. | Deposit date: | 2007-05-29 | Release date: | 2007-07-10 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Structural basis for nick recognition by a minimal pluripotent DNA ligase. Nat.Struct.Mol.Biol., 14, 2007
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1JR7
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5VZJ
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2HV9
| Encephalitozoon cuniculi mRNA Cap (Guanine-N7) Methyltransferase in complex with sinefungin | Descriptor: | SINEFUNGIN, mRNA cap guanine-N7 methyltransferase | Authors: | Lima, C.D. | Deposit date: | 2006-07-27 | Release date: | 2006-09-19 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Mutational Analysis of Encephalitozoon cuniculi mRNA Cap (Guanine-N7) Methyltransferase, Structure of the Enzyme Bound to Sinefungin, and Evidence That Cap Methyltransferase Is the Target of Sinefungin's Antifungal Activity J.Biol.Chem., 281, 2006
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7KMY
| Structure of Mtb Lpd bound to 010705 | Descriptor: | Dihydrolipoyl dehydrogenase, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... | Authors: | Lima, C.D. | Deposit date: | 2020-11-03 | Release date: | 2021-01-27 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.21 Å) | Cite: | Whole Cell Active Inhibitors of Mycobacterial Lipoamide Dehydrogenase Afford Selectivity over the Human Enzyme through Tight Binding Interactions. Acs Infect Dis., 7, 2021
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8CT4
| Cryo-EM structure of Mtb Lpd bound to inhibitor complex with 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide | Descriptor: | Dihydrolipoyl dehydrogenase, FLAVIN-ADENINE DINUCLEOTIDE, N~2~-(2-cyano-5-methyl-1H-indole-7-sulfonyl)-N~2~-methyl-N-[4-(oxetan-3-yl)-3,4-dihydro-2H-1,4-benzoxazin-7-yl]glycinamide | Authors: | Kochanczyk, T, Arango, N, Lima, C.D. | Deposit date: | 2022-05-13 | Release date: | 2022-05-25 | Last modified: | 2024-06-12 | Method: | ELECTRON MICROSCOPY (2.17 Å) | Cite: | Cryo-EM structure of Mtb Lpd bound to the inhibitor 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide at 2.17 Angstrom resolution Not published
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3UIO
| Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II | Descriptor: | E3 SUMO-protein ligase RanBP2, Ran GTPase-activating protein 1, SUMO-conjugating enzyme UBC9, ... | Authors: | Gareau, J.R, Reverter, D, Lima, C.D. | Deposit date: | 2011-11-05 | Release date: | 2011-12-28 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.602 Å) | Cite: | Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2. J.Biol.Chem., 287, 2012
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5FG1
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5FG0
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2FS2
| Structure of the E. coli PaaI protein from the phyenylacetic acid degradation operon | Descriptor: | Phenylacetic acid degradation protein paaI, SULFATE ION | Authors: | Kniewel, R, Buglino, J.A, Solorzano, V, Wu, J, Lima, C.D, Burley, S.K, New York SGX Research Center for Structural Genomics (NYSGXRC) | Deposit date: | 2006-01-20 | Release date: | 2006-02-07 | Last modified: | 2021-02-03 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structure, Function, and Mechanism of the Phenylacetate Pathway Hot Dog-fold Thioesterase PaaI J.Biol.Chem., 281, 2006
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4XQ0
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4XPZ
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6O83
| S. pombe ubiquitin E1~ubiquitin-AMP tetrahedral intermediate mimic | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine, ... | Authors: | Hann, Z.S, Lima, C.D. | Deposit date: | 2019-03-08 | Release date: | 2019-06-19 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (3.153 Å) | Cite: | Structural basis for adenylation and thioester bond formation in the ubiquitin E1. Proc.Natl.Acad.Sci.USA, 116, 2019
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6O82
| S. pombe ubiquitin E1 complex with a ubiquitin-AMP mimic | Descriptor: | 1,2-ETHANEDIOL, 5'-deoxy-5'-(sulfamoylamino)adenosine, MAGNESIUM ION, ... | Authors: | Olsen, S.K, Lima, C.D. | Deposit date: | 2019-03-08 | Release date: | 2019-06-19 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.604 Å) | Cite: | Structural basis for adenylation and thioester bond formation in the ubiquitin E1. Proc.Natl.Acad.Sci.USA, 116, 2019
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