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2Z33
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BU of 2z33 by Molmil
Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain
Descriptor: 5'-D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3', 5'-D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3', Phosphate regulon transcriptional regulatory protein phoB
Authors:Yamane, T, Okamura, H, Ikeguchi, M, Nishimura, Y, Kidera, A.
Deposit date:2007-05-31
Release date:2008-04-22
Last modified:2022-03-16
Method:SOLUTION NMR
Cite:Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment.
Proteins, 71, 2008
3KZA
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BU of 3kza by Molmil
Crystal structure of Gyuba, a patched chimera of b-lactglobulin
Descriptor: Beta-lactoglobulin
Authors:Tsuge, H, Ohtomo, H, Utsunomiya, H, Konuma, T, Ikeguchi, M.
Deposit date:2009-12-08
Release date:2010-12-22
Last modified:2021-11-10
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structure and stability of Gyuba, a patched chimera of b-lactoglobulin
Protein Sci., 20, 2011
1K85
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BU of 1k85 by Molmil
Solution structure of the fibronectin type III domain from Bacillus circulans WL-12 Chitinase A1.
Descriptor: CHITINASE A1
Authors:Jee, J.G, Ikegami, T, Hashimoto, M, Kawabata, T, Ikeguchi, M, Watanabe, T, Shirakawa, M.
Deposit date:2001-10-23
Release date:2002-12-18
Last modified:2022-02-23
Method:SOLUTION NMR
Cite:Solution Structure of the Fibronectin Type III Domain from Bacillus circulans WL-12 Chitinase A1
J.Biol.Chem., 277, 2002
3A57
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BU of 3a57 by Molmil
Crystal structure of Thermostable Direct Hemolysin
Descriptor: Thermostable direct hemolysin 2
Authors:Hashimoto, H, Yanagihara, I, Nakahira, K, Hamada, D, Ikegami, T, Mayanagi, K, Kaieda, S, Fukui, T, Ohnishi, K, Kajiyama, S, Yamane, T, Ikeguchi, M, Honda, T, Shimizu, T, Sato, M.
Deposit date:2009-08-03
Release date:2010-03-31
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin
J.Biol.Chem., 285, 2010
3VIQ
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BU of 3viq by Molmil
Crystal structure of Swi5-Sfr1 complex from fission yeast
Descriptor: GLYCEROL, Mating-type switching protein swi5, NITRATE ION, ...
Authors:Kuwabara, N, Murayama, Y, Hashimoto, H, Kokabu, Y, Ikeguchi, M, Sato, M, Mayanagi, K, Tsutsui, Y, Iwasaki, H, Shimizu, T.
Deposit date:2011-10-06
Release date:2012-08-22
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Mechanistic insights into the activation of Rad51-mediated strand exchange from the structure of a recombination activator, the Swi5-Sfr1 complex
Structure, 20, 2012
2NOO
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BU of 2noo by Molmil
Crystal Structure of Mutant NikA
Descriptor: IODIDE ION, NICKEL (II) ION, Nickel-binding periplasmic protein
Authors:Addy, C, Ohara, M, Kawai, F, Kidera, A, Ikeguchi, M, Fuchigami, S, Osawa, M, Shimada, I, Park, S.Y, Tame, J.R.H, Heddle, J.G.
Deposit date:2006-10-26
Release date:2007-01-23
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography.
Acta Crystallogr.,Sect.D, 63, 2007
2RPQ
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BU of 2rpq by Molmil
Solution Structure of a SUMO-interacting motif of MBD1-containing chromatin-associated factor 1 bound to SUMO-3
Descriptor: Activating transcription factor 7-interacting protein 1, Small ubiquitin-related modifier 2
Authors:Sekiyama, N, Ikegami, T, Yamane, T, Ikeguchi, M, Uchimura, Y, Baba, D, Ariyoshi, M, Tochio, H, Saitoh, H, Shirakawa, M.
Deposit date:2008-07-07
Release date:2008-10-07
Last modified:2015-12-09
Method:SOLUTION NMR
Cite:Structure of the small ubiquitin-like modifier (SUMO)-interacting motif of MBD1-containing chromatin-associated factor 1 bound to SUMO-3
J.Biol.Chem., 283, 2008
2RVQ
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BU of 2rvq by Molmil
Solution structure of the isolated histone H2A-H2B heterodimer
Descriptor: Histone H2A type 1-B/E, Histone H2B type 1-J
Authors:Moriwaki, Y, Yamane, T, Ohtomo, H, Ikeguchi, M, Kurita, J, Sato, M, Nagadoi, A, Shimojo, H, Nishimura, Y.
Deposit date:2016-03-28
Release date:2016-05-25
Method:SOLUTION NMR
Cite:Solution structure of the isolated histone H2A-H2B heterodimer
Sci Rep, 6, 2016
2RQ7
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BU of 2rq7 by Molmil
Solution structure of the epsilon subunit chimera combining the N-terminal beta-sandwich domain from T. Elongatus bp-1 f1 and the C-terminal alpha-helical domain from spinach chloroplast F1
Descriptor: ATP synthase epsilon chain,ATP synthase epsilon chain, chloroplastic
Authors:Yagi, H, Konno, H, Murakami-Fuse, T, Oroguchi, H, Akutsu, T, Ikeguchi, M, Hisabori, T.
Deposit date:2009-03-03
Release date:2010-01-12
Last modified:2020-01-01
Method:SOLUTION NMR
Cite:Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms.
Biochem.J., 425, 2010
2RQ6
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BU of 2rq6 by Molmil
Solution structure of the epsilon subunit of the F1-atpase from thermosynechococcus elongatus BP-1
Descriptor: ATP synthase epsilon chain
Authors:Yagi, H, Konno, H, Murakami-Fuse, T, Oroguchi, H, Akutsu, T, Ikeguchi, M, Hisabori, T.
Deposit date:2009-03-03
Release date:2010-01-12
Last modified:2022-03-16
Method:SOLUTION NMR
Cite:Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms.
Biochem.J., 425, 2010
5WVO
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BU of 5wvo by Molmil
Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3
Descriptor: DNA (cytosine-5)-methyltransferase 1, Histone H3.1, Ubiquitin, ...
Authors:Ishiyama, S, Nishiyama, A, Nakanishi, M, Arita, K.
Deposit date:2016-12-28
Release date:2017-11-15
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.997 Å)
Cite:Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance
Mol. Cell, 68, 2017
7BUL
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BU of 7bul by Molmil
Solution structure of the tandem PH and BSD1 domains of TFIIH p62
Descriptor: General transcription factor IIH subunit 1
Authors:Okuda, M, Nishimura, Y.
Deposit date:2020-04-07
Release date:2020-12-30
Last modified:2023-06-14
Method:SOLUTION NMR
Cite:Structural and dynamical insights into the PH domain of p62 in human TFIIH.
Nucleic Acids Res., 49, 2021
1V8Z
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BU of 1v8z by Molmil
X-ray crystal structure of the Tryptophan Synthase b2 Subunit from Hyperthermophile, Pyrococcus furiosus
Descriptor: PYRIDOXAL-5'-PHOSPHATE, SODIUM ION, Tryptophan synthase beta chain 1
Authors:Hioki, Y, Ogasahara, K, Lee, S.J, Ma, J, Ishida, M, Yamagata, Y, Matsuura, Y, Ota, M, Kuramitsu, S, Yutani, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2004-01-15
Release date:2005-02-22
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.21 Å)
Cite:The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors
Eur.J.Biochem., 271, 2004
6LVY
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BU of 6lvy by Molmil
Crystal structure of TLR7/Cpd-2 (SM-360320) complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 6-azanyl-2-(2-methoxyethoxy)-9-(phenylmethyl)-7H-purin-8-one, ...
Authors:Zhang, Z, Ohto, U, Shimizu, T.
Deposit date:2020-02-06
Release date:2020-11-11
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural analysis reveals TLR7 dynamics underlying antagonism.
Nat Commun, 11, 2020
6LW0
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BU of 6lw0 by Molmil
Crystal structure of TLR7/Cpd-6 (DSR-139293) complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-ethoxy-8-(5-fluoranylpyridin-3-yl)-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purin-6-amine, ...
Authors:Zhang, Z, Ohto, U, Shimizu, T.
Deposit date:2020-02-06
Release date:2020-11-11
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural analysis reveals TLR7 dynamics underlying antagonism.
Nat Commun, 11, 2020
6LW1
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BU of 6lw1 by Molmil
Cryo-EM structure of TLR7/Cpd-7 (DSR-139970) complex in open form
Descriptor: 2-ethoxy-8-(5-fluoranylpyridin-3-yl)-6-methyl-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purine, Toll-like receptor 7
Authors:Zhang, Z, Ohto, U, Shimizu, T.
Deposit date:2020-02-06
Release date:2020-11-11
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Structural analysis reveals TLR7 dynamics underlying antagonism.
Nat Commun, 11, 2020
6LVZ
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BU of 6lvz by Molmil
Crystal structure of TLR7/Cpd-3 (SM-394830) complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 6-azanyl-2-(2-methoxyethoxy)-9-(pyridin-3-ylmethyl)-7H-purin-8-one, ...
Authors:Zhang, Z, Ohto, U, Shimizu, T.
Deposit date:2020-02-06
Release date:2020-11-11
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.83 Å)
Cite:Structural analysis reveals TLR7 dynamics underlying antagonism.
Nat Commun, 11, 2020
6LVX
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BU of 6lvx by Molmil
Crystal structure of TLR7/Cpd-1 (SM-374527) complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 6-azanyl-2-butoxy-9-(phenylmethyl)-7H-purin-8-one, ...
Authors:Zhang, Z, Ohto, U, Shimizu, T.
Deposit date:2020-02-06
Release date:2020-11-11
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.77 Å)
Cite:Structural analysis reveals TLR7 dynamics underlying antagonism.
Nat Commun, 11, 2020
5B41
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BU of 5b41 by Molmil
Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3
Descriptor: (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor
Authors:Anami, Y, Itoh, T, Yamamoto, K.
Deposit date:2016-03-23
Release date:2016-12-07
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics
J.Med.Chem., 59, 2016
7FB7
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BU of 7fb7 by Molmil
Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 5-amino-2,4-dimethylpyridine, DIMETHYL SULFOXIDE, ...
Authors:Kori, S, Arita, K, Yoshimi, S.
Deposit date:2021-07-08
Release date:2022-01-05
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1.
Bioorg.Med.Chem., 52, 2021
6S58
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BU of 6s58 by Molmil
AvaII restriction endonuclease in the absence of nucleic acids
Descriptor: CALCIUM ION, Type II site-specific deoxyribonuclease, UNKNOWN ATOM OR ION
Authors:Kisiala, M, Kowalska, M, Korza, H, Czapinska, H, Bochtler, M.
Deposit date:2019-06-30
Release date:2020-05-20
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (2.32 Å)
Cite:Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation.
Nucleic Acids Res., 48, 2020
6S48
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BU of 6s48 by Molmil
AvaII RESTRICTION ENDONUCLEASE IN COMPLEX WITH PARTIALLY CLEAVED dsDNA
Descriptor: BETA-MERCAPTOETHANOL, CALCIUM ION, DNA (5'-D(*GP*AP*TP*G)-3'), ...
Authors:Kisiala, M, Kowalska, M, Korza, H, Czapinska, H, Bochtler, M.
Deposit date:2019-06-26
Release date:2020-05-20
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation.
Nucleic Acids Res., 48, 2020
7CQD
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BU of 7cqd by Molmil
The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 235 and 236
Descriptor: Heavy chain of antigen binding fragment, Fab of NZ-1, Light chain of antigen binding fragment, ...
Authors:Tamura-Sakaguchi, R, Aruga, R, Nogi, T.
Deposit date:2020-08-10
Release date:2021-05-19
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion.
Acta Crystallogr D Struct Biol, 77, 2021
7CQC
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BU of 7cqc by Molmil
The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 181 and 184
Descriptor: Heavy chain of antigen binding fragment, Fab of NZ-1, Light chain of antigen binding fragment, ...
Authors:Aruga, R, Tamura-Sakaguchi, R, Nogi, T.
Deposit date:2020-08-10
Release date:2021-05-19
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion.
Acta Crystallogr D Struct Biol, 77, 2021
7Y4Q
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BU of 7y4q by Molmil
Semaphorin 6D in complex with Plexin A1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Plexin-A1, ...
Authors:Tanaka, T, Neyazaki, M, Nogi, T.
Deposit date:2022-06-16
Release date:2022-10-19
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (4.7 Å)
Cite:Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D.
Protein Sci., 31, 2022

 

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