PDB: 55698 resultsInfo pagesStatus searchChemie searchBIRD

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9B5O	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from consensus Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (3.19 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway To be published
9B38	Kainate receptor GluK2 in complex with agonist glutamate with pseudo 4-fold symmetrical ligand-binding domain layer Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLUTAMIC ACID, ... Authors: Nadezhdin, K.D, Gangwar, S.P, Sobolevsky, A.I. Deposit date: 2024-03-18 Release date: 2024-05-22 Last modified: 2024-06-26 Method: ELECTRON MICROSCOPY (3.36 Å) Cite: Kainate receptor channel opening and gating mechanism. Nature, 630, 2024
9B5W	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from cluster 5 (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (3.96 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway To be published
8UOW	Structure of atypical asparaginase from Rhodospirillum rubrum (mutant Y21A) Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Asparaginase Authors: Lubkowski, J, Wlodawer, A, Zhang, D. Deposit date: 2023-10-20 Release date: 2024-04-03 Method: X-RAY DIFFRACTION (1.6 Å) Cite: RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases. Protein Sci., 33, 2024
8X51	Cryo-EM structure of Gabija GajA in complex with DNA(focused refinement) Descriptor: CALCIUM ION, DNA (5'-D(*AP*AP*AP*AP*AP*TP*AP*AP*CP*CP*GP*GP*GP*TP*TP*AP*TP*TP*AP*AP*A)-3'), DNA (5'-D(*TP*TP*TP*AP*AP*TP*AP*AP*CP*CP*CP*GP*GP*TP*TP*AP*TP*TP*TP*TP*T)-3'), ... Authors: Li, J, Wang, Z, Wang, L. Deposit date: 2023-11-16 Release date: 2024-02-28 Last modified: 2024-05-22 Method: ELECTRON MICROSCOPY (2.92 Å) Cite: Structures and activation mechanism of the Gabija anti-phage system. Nature, 629, 2024
9B55	Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 1 Descriptor: 4-aminobutanenitrile, E3 ubiquitin-protein ligase pub2, Ubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (3.23 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway To be published
9B5Q	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 2 map and model (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (2.95 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway To be published
9B57	Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 3 Descriptor: 4-aminobutanenitrile, E3 ubiquitin-protein ligase pub2, Ubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (3.37 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway To be published
8WDG	Subatomic crystal structure of glucose isomerase from Streptomyces rubiginosus Descriptor: MAGNESIUM ION, Xylitol, Xylose isomerase Authors: Nam, K.H. Deposit date: 2023-09-15 Release date: 2023-10-04 Last modified: 2024-04-17 Method: X-RAY DIFFRACTION (0.99 Å) Cite: Xylitol binding to the M1 site of glucose isomerase induces a conformational change in the substrate binding channel. Biochem.Biophys.Res.Commun., 682, 2023
9B5B	Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 7 Descriptor: 4-aminobutanenitrile, E3 ubiquitin-protein ligase pub2, Ubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (3.31 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway To be published
9B5M	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - consensus map and model Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (2.79 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway To be published
8UTG	An RNA G-Quadruplex from the NS5 gene in the West Nile Virus Genome Descriptor: AMMONIUM ION, POTASSIUM ION, RNA (5'-R(*UP*AP*UP*GP*GP*AP*AP*GP*AP*GP*GP*CP*GP*GP*UP*UP*GP*GP*UP*AP*U)-3') Authors: Terrell, J.R, Le, T.T, Wilson, W.D, Siemer, J.L. Deposit date: 2023-10-31 Release date: 2024-06-19 Last modified: 2024-07-17 Method: X-RAY DIFFRACTION (1.97 Å) Cite: Structure of an RNA G-quadruplex from the West Nile virus genome. Nat Commun, 15, 2024
9B39	Kainate receptor GluK2 in complex with agonist glutamate with asymmetric ligand-binding domain layer Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLUTAMIC ACID, ... Authors: Nadezhdin, K.D, Gangwar, S.P, Sobolevsky, A.I. Deposit date: 2024-03-18 Release date: 2024-05-22 Last modified: 2024-06-26 Method: ELECTRON MICROSCOPY (3.84 Å) Cite: Kainate receptor channel opening and gating mechanism. Nature, 630, 2024
9B5U	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from cluster 1 (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (3.67 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway To be published
8Y2H	GK tetramer of AtP5CS1 filament with adjacent hooks, reaction state Descriptor: ADENOSINE-5'-TRIPHOSPHATE, Delta-1-pyrroline-5-carboxylate synthase A Authors: Zhang, T, Guo, C.J, Liu, J.L. Deposit date: 2024-01-26 Release date: 2024-06-05 Last modified: 2024-07-10 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Dynamic Arabidopsis P5CS filament facilitates substrate channelling. Nat.Plants, 10, 2024
9B5A	Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 6 Descriptor: 4-aminobutanenitrile, E3 ubiquitin-protein ligase pub2, Ubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (3.65 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway To be published
9B59	Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 5 Descriptor: 4-aminobutanenitrile, E3 ubiquitin-protein ligase pub2, Ubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Method: ELECTRON MICROSCOPY (3.49 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway To be published
3W0Q	Crystal structure of a thermostable mutant of aminoglycoside phosphotransferase APH(4)-Ia (N203A), ternary complex with AMP-PNP and hygromycin B Descriptor: HYGROMYCIN B VARIANT, Hygromycin-B 4-O-kinase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Authors: Iino, D, Takakura, Y, Fukano, K, Sasaki, Y, Hoshino, T, Ohsawa, K, Nakamura, A, Yajima, S. Deposit date: 2012-11-02 Release date: 2013-08-07 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Crystal structures of the ternary complex of APH(4)-Ia/Hph with hygromycin B and an ATP analog using a thermostable mutant. J.Struct.Biol., 183, 2013
3VI0	Crystal structure of the O intermediate of the L93A mutant of bacteriorhodopsin Descriptor: 2,3-DI-PHYTANYL-GLYCEROL, 3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose, Bacteriorhodopsin, ... Authors: Kouyama, T, Zhang, J. Deposit date: 2011-09-13 Release date: 2012-06-13 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Crystal structure of the O intermediate of the Leu93Ala mutant of bacteriorhodopsin Proteins, 80, 2012
3W0O	Crystal structure of a thermostable mutant of aminoglycoside phosphotransferase APH(4)-Ia, ternary complex with ADP and hygromycin B Descriptor: ADENOSINE-5'-DIPHOSPHATE, HYGROMYCIN B VARIANT, Hygromycin-B 4-O-kinase Authors: Iino, D, Takakura, Y, Fukano, K, Sasaki, Y, Hoshino, T, Ohsawa, K, Nakamura, A, Yajima, S. Deposit date: 2012-11-02 Release date: 2013-08-07 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (1.5 Å) Cite: Crystal structures of the ternary complex of APH(4)-Ia/Hph with hygromycin B and an ATP analog using a thermostable mutant. J.Struct.Biol., 183, 2013
3W0N	Crystal structure of a thermostable mutant of aminoglycoside phosphotransferase APH(4)-Ia, ternary complex with AMP-PNP and hygromycin B Descriptor: HYGROMYCIN B VARIANT, Hygromycin-B 4-O-kinase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Authors: Iino, D, Takakura, Y, Fukano, K, Sasaki, Y, Hoshino, T, Ohsawa, K, Nakamura, A, Yajima, S. Deposit date: 2012-11-02 Release date: 2013-08-07 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Crystal structures of the ternary complex of APH(4)-Ia/Hph with hygromycin B and an ATP analog using a thermostable mutant. J.Struct.Biol., 183, 2013
3VW2	Crystal Strucuture of The Berberine-bound Form of RamR (Transcriptional Regurator of TetR Family) from Salmonella Typhimurium Descriptor: BERBERINE, Putative regulatory protein, SULFATE ION Authors: Sakurai, K, Nikaido, E, Nakashima, R, Yamasaki, S, Yamaguchi, A, Nishino, K. Deposit date: 2012-07-30 Release date: 2013-07-03 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (2.34 Å) Cite: The crystal structure of multidrug-resistance regulator RamR with multiple drugs Nat Commun, 4, 2013
3W0S	Crystal structure of aminoglycoside phosphotransferase APH(4)-Ia, ternary complex with AMP-PNP and hygromycin B Descriptor: HYGROMYCIN B VARIANT, Hygromycin-B 4-O-kinase, MAGNESIUM ION, ... Authors: Iino, D, Takakura, Y, Fukano, K, Sasaki, Y, Hoshino, T, Ohsawa, K, Nakamura, A, Yajima, S. Deposit date: 2012-11-02 Release date: 2013-08-07 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (1.77 Å) Cite: Crystal structures of the ternary complex of APH(4)-Ia/Hph with hygromycin B and an ATP analog using a thermostable mutant. J.Struct.Biol., 183, 2013
3W0P	Crystal structure of a thermostable mutant of aminoglycoside phosphotransferase APH(4)-Ia (D198A), ternary complex with ADP and hygromycin B Descriptor: ADENOSINE-5'-DIPHOSPHATE, HYGROMYCIN B VARIANT, Hygromycin-B 4-O-kinase Authors: Iino, D, Takakura, Y, Fukano, K, Sasaki, Y, Hoshino, T, Ohsawa, K, Nakamura, A, Yajima, S. Deposit date: 2012-11-02 Release date: 2013-08-07 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (2 Å) Cite: Crystal structures of the ternary complex of APH(4)-Ia/Hph with hygromycin B and an ATP analog using a thermostable mutant. J.Struct.Biol., 183, 2013
7PXW	LPMO, expressed in E.coli, in complex with Cellotetraose Descriptor: Auxiliary activity 9, CHLORIDE ION, COPPER (II) ION, ... Authors: Banerjee, S, Muderspach, S.J, Tandrup, T, Ipsen, J, Rollan, C.H, Norholm, M, Johansen, K.S, Lo Leggio, L. Deposit date: 2021-10-08 Release date: 2022-08-24 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (1.4 Å) Cite: Changes in active-site geometry on X-ray photoreduction of a lytic polysaccharide monooxygenase active-site copper and saccharide binding. Iucrj, 9, 2022

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