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PDB: 63 results
1J1G
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BU of 1j1g by Molmil
Crystal structure of the RNase MC1 mutant N71S in complex with 5'-GMP
Descriptor: GUANOSINE-5'-MONOPHOSPHATE, Ribonuclease MC1
Authors:Numata, T, Suzuki, A, Kakuta, Y, Kimura, K, Yao, M, Tanaka, I, Yoshida, Y, Ueda, T, Kimura, M.
Deposit date:2002-12-04
Release date:2003-05-20
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-GMP: Structural Basis for Alterations in Substrate Specificity
Biochemistry, 42, 2003
1J1F
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BU of 1j1f by Molmil
Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP
Descriptor: GUANOSINE-5'-MONOPHOSPHATE, RIBONUCLEASE MC1
Authors:Numata, T, Suzuki, A, Kakuta, Y, Kimura, K, Yao, M, Tanaka, I, Yoshida, Y, Ueda, T, Kimura, M.
Deposit date:2002-12-03
Release date:2003-05-20
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-GMP: Structural Basis for Alterations in Substrate Specificity
Biochemistry, 42, 2003
4DWX
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BU of 4dwx by Molmil
Crystal Structure of a Family GH-19 Chitinase from rye seeds
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Basic endochitinase C, SULFATE ION, ...
Authors:Numata, T, Umemoto, N, Ohnuma, T, Fukamizo, T.
Deposit date:2012-02-27
Release date:2012-08-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structure and chitin oligosaccharide-binding mode of a 'loopful' family GH19 chitinase from rye, Secale cereale, seeds
Febs J., 279, 2012
4DYG
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BU of 4dyg by Molmil
Crystal Structure of a Family GH-19 Chitinase from rye seeds in complex with (GlcNAc)4
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Basic endochitinase C, ...
Authors:Numata, T, Umemoto, N, Ohnuma, T, Fukamizo, T.
Deposit date:2012-02-29
Release date:2012-08-15
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structure and chitin oligosaccharide-binding mode of a 'loopful' family GH19 chitinase from rye, Secale cereale, seeds
Febs J., 279, 2012
4QTS
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BU of 4qts by Molmil
Crystal structure of Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex
Descriptor: CRISPR type III-associated RAMP protein Csm3, CRISPR type III-associated RAMP protein Csm4, ZINC ION
Authors:Numata, T, Inanaga, H, Osawa, T.
Deposit date:2014-07-09
Release date:2014-12-24
Last modified:2022-08-24
Method:X-RAY DIFFRACTION (3.105 Å)
Cite:Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex.
J.Mol.Biol., 427, 2015
4IJ4
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BU of 4ij4 by Molmil
Crystal Structure of a Family GH19 chitinase from Bryum coronatum in complex with (GlcNAc)4
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Chitinase A
Authors:Numata, T, Umemoto, N, Ohnuma, T, Fukamizo, T.
Deposit date:2012-12-21
Release date:2014-03-26
Last modified:2022-08-24
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center.
Biochim.Biophys.Acta, 1844, 2014
3WIJ
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BU of 3wij by Molmil
Crystal structure of a plant class V chitinase mutant from Cycas revoluta in complex with (GlcNAc)3
Descriptor: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, ...
Authors:Numata, T, Osawa, T, Umemoto, N, Ohnuma, T, Fukamizo, T.
Deposit date:2013-09-13
Release date:2014-09-17
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:Crystal structure of a plant class V chitinase mutant from Cycas revoluta in complex with (GlcNAc)3
To be Published
3WH1
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Crystal Structure of a Family GH19 Chitinase from Bryum coronatum in complex with (GlcNAc)4 at 1.0 A resolution
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Chitinase A
Authors:Numata, T, Umemoto, N, Ohnuma, T, Fukamizo, T.
Deposit date:2013-08-21
Release date:2014-03-26
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1 Å)
Cite:Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center.
Biochim.Biophys.Acta, 1844, 2014
7E9E
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BU of 7e9e by Molmil
Crystal structure of a class I PreQ1 riboswitch aptamer (ab13-14) complexed with a cognate ligand-derived photoaffinity probe
Descriptor: 2-azanyl-5-[[2-(3-but-3-ynyl-1,2-diazirin-3-yl)ethylamino]methyl]-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one, 33-mer RNA, MAGNESIUM ION, ...
Authors:Numata, T, Schneekloth, J.S.
Deposit date:2021-03-04
Release date:2021-11-17
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.57 Å)
Cite:A chemical probe based on the PreQ 1 metabolite enables transcriptome-wide mapping of binding sites.
Nat Commun, 12, 2021
7E9I
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BU of 7e9i by Molmil
Crystal structure of a class I PreQ1 riboswitch aptamer (wild-type) complexed with a cognate ligand-derived photoaffinity probe
Descriptor: 2-azanyl-5-[[2-(3-but-3-ynyl-1,2-diazirin-3-yl)ethylamino]methyl]-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one, 33-mer RNA, SULFATE ION
Authors:Numata, T, Schneekloth, J.S.
Deposit date:2021-03-04
Release date:2021-11-17
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:A chemical probe based on the PreQ 1 metabolite enables transcriptome-wide mapping of binding sites.
Nat Commun, 12, 2021
6AE2
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BU of 6ae2 by Molmil
Crystal structure of Csm3 of the type III-A CRISPR-Cas effector complex
Descriptor: Csm3
Authors:Numata, T.
Deposit date:2018-08-03
Release date:2019-01-23
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.701 Å)
Cite:Crystal Structures of Csm2 and Csm3 in the Type III-A CRISPR-Cas Effector Complex.
J. Mol. Biol., 431, 2019
6AE1
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BU of 6ae1 by Molmil
Crystal structure of Csm2 of the type III-A CRISPR-Cas effector complex
Descriptor: CRISPR-associated protein, TM1810 family
Authors:Numata, T.
Deposit date:2018-08-03
Release date:2019-01-23
Last modified:2019-02-27
Method:X-RAY DIFFRACTION (2.405 Å)
Cite:Crystal Structures of Csm2 and Csm3 in the Type III-A CRISPR-Cas Effector Complex.
J. Mol. Biol., 431, 2019
3W2W
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BU of 3w2w by Molmil
Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to ATP
Descriptor: ADENOSINE-5'-TRIPHOSPHATE, CRISPR system Cmr subunit Cmr2, CRISPR system Cmr subunit Cmr3, ...
Authors:Numata, T, Osawa, T.
Deposit date:2012-12-06
Release date:2013-10-16
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal Structure of the Cmr2-Cmr3 Subcomplex in the CRISPR-Cas RNA Silencing Effector Complex.
J.Mol.Biol., 425, 2013
3W2V
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BU of 3w2v by Molmil
Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP
Descriptor: CRISPR system Cmr subunit Cmr2, CRISPR system Cmr subunit Cmr3, ZINC ION, ...
Authors:Numata, T, Osawa, T.
Deposit date:2012-12-06
Release date:2013-10-16
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Crystal Structure of the Cmr2-Cmr3 Subcomplex in the CRISPR-Cas RNA Silencing Effector Complex.
J.Mol.Biol., 425, 2013
6E1V
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BU of 6e1v by Molmil
Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 3: 2-[(9H-carbazol-3-yl)oxy]-N,N-dimethylethan-1-amine
Descriptor: 2-[(9H-carbazol-3-yl)oxy]-N,N-dimethylethan-1-amine, RNA (33-MER)
Authors:Numata, T, Connelly, C.M, Schneekloth, J.S, Ferre-D'Amare, A.R.
Deposit date:2018-07-10
Release date:2019-04-10
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.56 Å)
Cite:Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun, 10, 2019
6E1S
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BU of 6e1s by Molmil
Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 1: 2-[(dibenzo[b,d]furan-2-yl)oxy]ethan-1-amine
Descriptor: 2-[(dibenzo[b,d]furan-2-yl)oxy]ethan-1-amine, RNA (33-MER)
Authors:Numata, T, Connelly, C.M, Schneekloth, J.S, Ferre-D'Amare, A.R.
Deposit date:2018-07-10
Release date:2019-04-10
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun, 10, 2019
6E1T
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BU of 6e1t by Molmil
Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 1: 2-[(dibenzo[b,d]furan-2-yl)oxy]ethan-1-amine
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-[(dibenzo[b,d]furan-2-yl)oxy]ethan-1-amine, MAGNESIUM ION, ...
Authors:Numata, T, Connelly, C.M, Schneekloth, J.S, Ferre-D'Amare, A.R.
Deposit date:2018-07-10
Release date:2019-04-10
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun, 10, 2019
6E1W
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BU of 6e1w by Molmil
Crystal structure of a class I PreQ1 riboswitch complexed with PreQ1
Descriptor: 2-amino-5-(aminomethyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one, ACETATE ION, MAGNESIUM ION, ...
Authors:Numata, T, Connelly, C.M, Schneekloth, J.S, Ferre-D'Amare, A.R.
Deposit date:2018-07-10
Release date:2019-04-10
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.69 Å)
Cite:Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun, 10, 2019
6E1U
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BU of 6e1u by Molmil
Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 2: 2-[(dibenzo[b,d]furan-2-yl)oxy]-N,N-dimethylethan-1-amine
Descriptor: 2-[(dibenzo[b,d]furan-2-yl)oxy]-N,N-dimethylethan-1-amine, MAGNESIUM ION, RNA (33-MER)
Authors:Numata, T, Connelly, C.M, Schneekloth, J.S, Ferre-D'Amare, A.R.
Deposit date:2018-07-10
Release date:2019-04-10
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun, 10, 2019
2D1P
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BU of 2d1p by Molmil
crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification
Descriptor: Hypothetical UPF0116 protein yheM, Hypothetical UPF0163 protein yheN, Hypothetical protein yheL, ...
Authors:Numata, T, Fukai, S, Ikeuchi, Y, Suzuki, T, Nureki, O.
Deposit date:2005-08-30
Release date:2006-02-28
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Structural Basis for Sulfur Relay to RNA Mediated by Heterohexameric TusBCD Complex
Structure, 14, 2006
2DER
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BU of 2der by Molmil
Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the initial tRNA binding state
Descriptor: PHOSPHATE ION, SULFATE ION, tRNA, ...
Authors:Numata, T, Ikeuchi, Y, Fukai, S, Suzuki, T, Nureki, O.
Deposit date:2006-02-17
Release date:2006-08-15
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Snapshots of tRNA sulphuration via an adenylated intermediate
Nature, 442, 2006
2DET
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BU of 2det by Molmil
Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the pre-reaction state
Descriptor: SULFATE ION, tRNA, tRNA-specific 2-thiouridylase mnmA
Authors:Numata, T, Ikeuchi, Y, Fukai, S, Suzuki, T, Nureki, O.
Deposit date:2006-02-17
Release date:2006-08-15
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (3.4 Å)
Cite:Snapshots of tRNA sulphuration via an adenylated intermediate
Nature, 442, 2006
2DEU
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BU of 2deu by Molmil
Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the adenylated intermediate state
Descriptor: ADENOSINE MONOPHOSPHATE, SULFATE ION, tRNA, ...
Authors:Numata, T, Ikeuchi, Y, Fukai, S, Suzuki, T, Nureki, O.
Deposit date:2006-02-17
Release date:2006-08-15
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (3.4 Å)
Cite:Snapshots of tRNA sulphuration via an adenylated intermediate
Nature, 442, 2006
3ALF
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BU of 3alf by Molmil
Crystal Structure of Class V Chitinase from Nicotiana tobaccum
Descriptor: 1,2-ETHANEDIOL, Chitinase, class V, ...
Authors:Numata, T, Osawa, T, Ohnuma, T, Fukamizo, T.
Deposit date:2010-08-03
Release date:2011-03-23
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Crystal structure and mode of action of a class V chitinase from Nicotiana tabacum
Plant Mol.Biol., 75, 2011
3ALG
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BU of 3alg by Molmil
Crystal Structure of Class V Chitinase (E115Q mutant) from Nicotiana tobaccum in complex with NAG4
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Chitinase, ...
Authors:Numata, T, Osawa, T, Ohnuma, T, Fukamizo, T.
Deposit date:2010-08-03
Release date:2011-03-23
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structure and mode of action of a class V chitinase from Nicotiana tabacum
Plant Mol.Biol., 75, 2011

 

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