6TVK
 
 | | Alpha-L-fucosidase isoenzyme 2 from Paenibacillus thiaminolyticus | | Descriptor: | Alpha-L-fucosidase, GLYCEROL, HEXATANTALUM DODECABROMIDE, ... | | Authors: | Kovalova, T, Koval, T, Lipovova, P, Dohnalek, J. | | Deposit date: | 2020-01-09 | | Release date: | 2021-07-21 | | Last modified: | 2022-05-18 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | The first structure-function study of GH151 alpha-l-fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity
Febs J., 2022
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6GN6
 | | Alpha-L-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus | | Descriptor: | Alpha-L-fucosidase, DI(HYDROXYETHYL)ETHER, HEXAETHYLENE GLYCOL, ... | | Authors: | Kovalova, T, Koval, T, Lipovova, P, Dohnalek, J. | | Deposit date: | 2018-05-30 | | Release date: | 2018-12-26 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Active site complementation and hexameric arrangement in the GH family 29; a structure-function study of alpha-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus.
Glycobiology, 29, 2019
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4DJ4
 | | X-ray structure of mutant N211D of bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Nuclease, ... | | Authors: | Koval, T, Stepankova, A, Lipovova, P, Podzimek, T, Matousek, J, Duskova, J, Skalova, T, Hasek, J, Dohnalek, J. | | Deposit date: | 2012-02-01 | | Release date: | 2012-11-07 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis.
Acta Crystallogr.,Sect.D, 69, 2013
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6I3L
 | | Bilirubin oxidase from Myrothecium verrucaria, mutant W396F | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Bilirubin oxidase, COPPER (II) ION, ... | | Authors: | Koval, T, Svecova, L, Skalova, T, Kolenko, P, Duskova, J, Ostergaard, L.H, Dohnalek, J. | | Deposit date: | 2018-11-06 | | Release date: | 2019-10-02 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer.
Sci Rep, 9, 2019
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6I3K
 | | Bilirubin oxidase from Myrothecium verrucaria, mutant W396A in complex with ferricyanide | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Bilirubin oxidase, COPPER (II) ION, ... | | Authors: | Koval, T, Svecova, L, Skalova, T, Kolenko, P, Duskova, J, Ostergaard, L.H, Dohnalek, J. | | Deposit date: | 2018-11-06 | | Release date: | 2019-10-02 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer.
Sci Rep, 9, 2019
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8A5R
 | | Crystal structure of light-activated DNA-binding protein EL222 from Erythrobacter litoralis crystallized and measured in dark. | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, FLAVIN MONONUCLEOTIDE, ... | | Authors: | Koval, T, Chaudhari, A, Fuertes, G, Andersson, I, Dohnalek, J. | | Deposit date: | 2022-06-15 | | Release date: | 2023-07-05 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | EL222 from Erythrobacter litoralis.
To Be Published
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8A5S
 | | Crystal structure of light-activated DNA-binding protein EL222 from Erythrobacter litoralis crystallized in dark, measured illuminated. | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, FLAVIN MONONUCLEOTIDE, ... | | Authors: | Koval, T, Chaudhari, A, Fuertes, G, Andersson, I, Dohnalek, J. | | Deposit date: | 2022-06-15 | | Release date: | 2023-07-05 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | EL222 from Erythrobacter litoralis.
To Be Published
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3SNG
 | | X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato) | | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, SULFATE ION, ... | | Authors: | Koval, T, Stepankova, A, Lipovova, P, Podzimek, T, Matousek, J, Duskova, J, Skalova, T, Hasek, J, Dohnalek, J. | | Deposit date: | 2011-06-29 | | Release date: | 2012-07-04 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.16 Å) | | Cite: | Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis.
Acta Crystallogr.,Sect.D, 69, 2013
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5FBB
 | | S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine 5'-monophosphate | | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL, ... | | Authors: | Koval, T, Oestergaard, L.H, Dohnalek, J. | | Deposit date: | 2015-12-14 | | Release date: | 2016-12-28 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
PLoS ONE, 11, 2016
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5FBG
 | | S1 nuclease from Aspergillus oryzae, mutant D65N, in complex with phosphate, 2'-deoxycytidine and 2'-deoxyguanosine. | | Descriptor: | 2'-DEOXY-GUANOSINE, 2'-DEOXYCYTIDINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Koval, T, Oestergaard, L.H, Dohnalek, J. | | Deposit date: | 2015-12-14 | | Release date: | 2016-12-28 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.97 Å) | | Cite: | Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
PLoS ONE, 11, 2016
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5FB9
 | | S1 nuclease from Aspergillus oryzae with unoccupied active site | | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, Nuclease S1, ... | | Authors: | Koval, T, Oestergaard, L.H, Dohnalek, J. | | Deposit date: | 2015-12-14 | | Release date: | 2016-12-28 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
PLoS ONE, 11, 2016
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5FBC
 | | S1 nuclease from Aspergillus oryzae in complex with 2'-deoxyadenosine-5'-thio-monophosphate (5'dAMP(S)). | | Descriptor: | 2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | | Authors: | Koval, T, Oestergaard, L.H, Dohnalek, J. | | Deposit date: | 2015-12-14 | | Release date: | 2016-12-28 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
PLoS ONE, 11, 2016
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5FBF
 | | S1 nuclease from Aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate | | Descriptor: | 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE, 2-acetamido-2-deoxy-beta-D-glucopyranose, Nuclease S1, ... | | Authors: | Koval, T, Oestergaard, L.H, Dohnalek, J. | | Deposit date: | 2015-12-14 | | Release date: | 2016-12-28 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.04 Å) | | Cite: | Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
PLoS ONE, 11, 2016
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5FBA
 | | S1 nuclease from Aspergillus oryzae in complex with phosphate | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Nuclease S1, ... | | Authors: | Koval, T, Oestergaard, L.H, Dohnalek, J. | | Deposit date: | 2015-12-14 | | Release date: | 2016-12-28 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
PLoS ONE, 11, 2016
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5FBD
 | | S1 nuclease from Aspergillus oryzae in complex with phosphate and 2'-deoxycytidine | | Descriptor: | 2'-DEOXYCYTIDINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, Nuclease S1, ... | | Authors: | Koval, T, Oestergaard, L.H, Dohnalek, J. | | Deposit date: | 2015-12-14 | | Release date: | 2016-12-28 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
PLoS ONE, 11, 2016
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7Q21
 | | III2-IV2 respiratory supercomplex from Corynebacterium glutamicum | | Descriptor: | (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate, (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate, (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate, ... | | Authors: | Kovalova, T, Moe, A, Krol, S, Yanofsky, D.J, Bott, M, Sjostrand, D, Rubinstein, J.L, Hogbom, M, Brzezinski, P. | | Deposit date: | 2021-10-22 | | Release date: | 2022-02-02 | | Last modified: | 2022-03-16 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | The respiratory supercomplex from C. glutamicum.
Structure, 30, 2022
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8OVD
 | | Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis | | Descriptor: | (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate, (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate, (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate, ... | | Authors: | Kovalova, T, Krol, S, Sjostrand, D, Riepl, D, Gamiz-Hernandez, A, Brzezinski, P, Kaila, V, Hogbom, M. | | Deposit date: | 2023-04-25 | | Release date: | 2024-07-17 | | Method: | ELECTRON MICROSCOPY (2.3 Å) | | Cite: | Long-range charge transfer mechanism of the III 2 IV 2 mycobacterial supercomplex.
Nat Commun, 15, 2024
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8OVC
 | | Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis | | Descriptor: | (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate, (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate, (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate, ... | | Authors: | Kovalova, T, Krol, S, Sjostrand, D, Riepl, D, Gamiz-Hernandez, A, Brzezinski, P, Kaila, V, Hogbom, M. | | Deposit date: | 2023-04-25 | | Release date: | 2024-07-17 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | Long-range charge transfer mechanism of the III 2 IV 2 mycobacterial supercomplex.
Nat Commun, 15, 2024
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7AA2
 | | Chaetomium thermophilum FAD-dependent oxidoreductase in complex with ABTS | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 3-ETHYL-2-[(2Z)-2-(3-ETHYL-6-SULFO-1,3-BENZOTHIAZOL-2(3H)-YLIDENE)HYDRAZINO]-6-SULFO-3H-1,3-BENZOTHIAZOL-1-IUM, ... | | Authors: | Svecova, L, Skalova, T, Kolenko, P, Koval, T, Oestergaard, L.H, Dohnalek, J. | | Deposit date: | 2020-09-03 | | Release date: | 2021-05-26 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum.
Acta Crystallogr D Struct Biol, 77, 2021
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7QTB
 | | S1 nuclease from Aspergillus oryzae in complex with cytidine-5'-monophosphate | | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Adamkova, K, Koval, T, Kolenko, P, Oestergaard, L.H, Dohnalek, J. | | Deposit date: | 2022-01-14 | | Release date: | 2022-11-09 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.04 Å) | | Cite: | Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects.
Acta Crystallogr D Struct Biol, 78, 2022
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7QTA
 | | S1 nuclease from Aspergillus oryzae in complex with uridine | | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, Nuclease S1, ... | | Authors: | Adamkova, K, Koval, T, Kolenko, P, Oestergaard, L.H, Dohnalek, J. | | Deposit date: | 2022-01-14 | | Release date: | 2022-11-09 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.06 Å) | | Cite: | Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects.
Acta Crystallogr D Struct Biol, 78, 2022
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5J2S
 | | NKR-P1B from Rattus norvegicus | | Descriptor: | Killer cell lectin-like receptor subfamily B member 1B allele A, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | | Authors: | Skalova, T, Vanek, O, Blaha, J, Duskova, J, Hasek, J, Koval, T, Dohnalek, J. | | Deposit date: | 2016-03-30 | | Release date: | 2017-10-11 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure of NKR-P1B from Rattus norvegicus
To Be Published
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6I3J
 | | Bilirubin oxidase from Myrothecium verrucaria in complex with ferricyanide | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Bilirubin oxidase, CHLORIDE ION, ... | | Authors: | Svecova, L, Koval, T, Skalova, T, Kolenko, P, Duskova, J, Ostergaard, L.H, Dohnalek, J. | | Deposit date: | 2018-11-06 | | Release date: | 2019-10-02 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (2.59 Å) | | Cite: | Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer.
Sci Rep, 9, 2019
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5MGT
 | | Complex of human NKR-P1 and LLT1 in deglycosylated forms | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, C-type lectin domain family 2 member D, CHLORIDE ION, ... | | Authors: | Blaha, J, Skalova, T, Stransky, J, Koval, T, Hasek, J, Yuguang, Z, Harlos, K, Vanek, O, Dohnalek, J. | | Deposit date: | 2016-11-22 | | Release date: | 2018-06-06 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.
Nat Commun, 13, 2022
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5MGS
 | | Human receptor NKR-P1 in deglycosylated form, extracellular domain | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Killer cell lectin-like receptor subfamily B member 1 | | Authors: | Skalova, T, Blaha, J, Stransky, J, Koval, T, Hasek, J, Yuguang, Z, Harlos, K, Vanek, O, Dohnalek, J. | | Deposit date: | 2016-11-22 | | Release date: | 2018-05-23 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.
Nat Commun, 13, 2022
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