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3VZ7
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BU of 3vz7 by Molmil
Crystal Structure Analysis of the mini-chaperonin variant with Pro 187 Gly
Descriptor: 60 kDa chaperonin
Authors:Saijo, S, Sato, T.
Deposit date:2012-10-09
Release date:2013-11-13
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Binding Energy(BE) from Crystal Packing of Mini-chaperones (mcpn) Provided Insights into the Allosteric Interaction of GroEL/ES Complex
To be Published
3VZ6
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BU of 3vz6 by Molmil
Crystal Structure Analysis of the Mini-chaperonines, variant with Gly 184 replaced with Ile and Leu 185 replaced Val and Val 186 replaced with Leu.
Descriptor: 60 kDa chaperonin
Authors:Saijo, S, Sato, T.
Deposit date:2012-10-09
Release date:2013-11-13
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Binding Energy(BE) from Crystal Packing of Mini-chaperones (mcpn) Provided Insights into the Allosteric Interaction of GroEL/ES Complex
To be Published
3VJF
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BU of 3vjf by Molmil
Crystal structure of de novo 4-helix bundle protein WA20
Descriptor: POTASSIUM ION, WA20
Authors:Arai, R, Kimura, A, Kobayashi, N, Matsuo, K, Sato, T, Wang, A.F, Platt, J.M, Bradley, L.H, Hecht, M.H.
Deposit date:2011-10-18
Release date:2012-03-28
Last modified:2024-10-30
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Domain-swapped dimeric structure of a stable and functional de novo four-helix bundle protein, WA20
J.Phys.Chem.B, 116, 2012
7BPG
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BU of 7bpg by Molmil
Structure of serinol nucleic acid - RNA complex
Descriptor: CALCIUM ION, RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3'), SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)
Authors:Kamiya, Y, Satoh, T, Kodama, A, Suzuki, T, Uchiyama, S, Kato, K, Asanuma, H.
Deposit date:2020-03-22
Release date:2020-11-25
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA
Commun Chem, 2020
7BPF
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BU of 7bpf by Molmil
Structure of L-threoninol nucleic acid - RNA complex
Descriptor: L-aTNA (3'-(*GP*CP*AP*GP*CP*AP*GP*C)-1'), RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
Authors:Kamiya, Y, Satoh, T, Kodama, A, Suzuki, T, Uchiyama, S, Kato, K, Asanuma, H.
Deposit date:2020-03-22
Release date:2020-11-25
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA
Commun Chem, 2020
5BW7
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BU of 5bw7 by Molmil
Crystal structure of nonfucosylated Fc Y296W mutant complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Isoda, Y, Yagi, H, Satoh, T, Shibata-Koyama, M, Masuda, K, Satoh, M, Kato, K, Iida, S.
Deposit date:2015-06-06
Release date:2015-10-14
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3 Å)
Cite:Importance of the Side Chain at Position 296 of Antibody Fc in Interactions with Fc gamma RIIIa and Other Fc gamma Receptors
Plos One, 10, 2015
5WTQ
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BU of 5wtq by Molmil
Crystal structure of human proteasome-assembling chaperone PAC4
Descriptor: CHLORIDE ION, NICKEL (II) ION, Proteasome assembly chaperone 4
Authors:Kurimoto, E, Satoh, T, Ito, Y, Ishihara, E, Tanaka, K, Kato, K.
Deposit date:2016-12-13
Release date:2017-03-22
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation
Protein Sci., 26, 2017
2RUF
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BU of 2ruf by Molmil
Solution structure of the a' domain of thermophilic fungal protein disulfide (reduced form, 303K)
Descriptor: Protein disulfide-isomerase
Authors:Inagaki, K, Satoh, T, Kato, K.
Deposit date:2014-03-31
Release date:2015-05-20
Last modified:2024-05-15
Method:SOLUTION NMR
Cite:Redox-coupled structural changes of the catalytic a' domain of protein disulfide isomerase.
Febs Lett., 589, 2015
2RUE
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BU of 2rue by Molmil
Solution structure of the a' domain of thermophilic fungal protein disulfide (oxidized form, 303K)
Descriptor: Protein disulfide-isomerase
Authors:Inagaki, K, Satoh, T, Kato, K.
Deposit date:2014-03-27
Release date:2015-05-20
Last modified:2023-06-14
Method:SOLUTION NMR
Cite:Redox-coupled structural changes of the catalytic a' domain of protein disulfide isomerase.
Febs Lett., 589, 2015
5CRW
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BU of 5crw by Molmil
Crystal structure of the b'-a' domain of oxidized protein disulfide isomerase complexed with alpha-synuclein peptide (31-41)
Descriptor: Peptide from Alpha-synuclein, Protein disulfide-isomerase
Authors:Yagi-Utsumi, M, Satoh, T, Kato, K.
Deposit date:2015-07-23
Release date:2015-09-09
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural basis of redox-dependent substrate binding of protein disulfide isomerase.
Sci Rep, 5, 2015
7CAP
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BU of 7cap by Molmil
Cyclic Lys48-linked triubiquitin
Descriptor: Ubiquitin, ZINC ION
Authors:Hiranyakorn, M, Yanaka, S, Satoh, T, Wilasri, T, Jityuti, B, Yagi-Utsumi, T, Kato, K.
Deposit date:2020-06-09
Release date:2020-08-19
Last modified:2024-10-09
Method:X-RAY DIFFRACTION (1.33 Å)
Cite:NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains.
Int J Mol Sci, 21, 2020
8IC9
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BU of 8ic9 by Molmil
Lys48-linked K48C-diubiquitin
Descriptor: Polyubiquitin-B, Ubiquitin
Authors:Hiranyakorn, M, Yagi-Utsumi, M, Yanaka, S, Ohtsuka, N, Momiyama, N, Satoh, T, Kato, K.
Deposit date:2023-02-11
Release date:2023-04-26
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:Mutational and Environmental Effects on the Dynamic Conformational Distributions of Lys48-Linked Ubiquitin Chains.
Int J Mol Sci, 24, 2023
7DBT
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BU of 7dbt by Molmil
Crystal structure of catalytic domain of Anhydrobiosis-related Mn-dependent Peroxidase (AMNP) from Ramazzottius varieornatus (Mn2+-bound form)
Descriptor: AMNP/g12777, MANGANESE (II) ION
Authors:Yoshida, Y, Satoh, T, Ota, C, Tanaka, S, Horikawa, D.D, Tomita, M, Kato, K, Arakawa, K.
Deposit date:2020-10-21
Release date:2021-10-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades.
Bmc Genomics, 23, 2022
7DBU
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BU of 7dbu by Molmil
Crystal structure of catalytic domain of Anhydrobiosis-related Mn-dependent Peroxidase (AMNP) from Ramazzottius varieornatus (Zn2+-bound form)
Descriptor: AMNP/g12777, ZINC ION
Authors:Yoshida, Y, Satoh, T, Ota, C, Tanaka, S, Horikawa, D.D, Tomita, M, Kato, K, Arakawa, K.
Deposit date:2020-10-21
Release date:2021-10-06
Last modified:2024-10-09
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades.
Bmc Genomics, 23, 2022
5Y9N
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BU of 5y9n by Molmil
Crystal structure of Pyrococcus furiosus PbaA (monoclinic form), an archaeal homolog of proteasome-assembly chaperone
Descriptor: CHLORIDE ION, PbaA
Authors:Yagi-Utsumi, M, Sikdar, A, Kozai, T, Inoue, R, Sugiyama, M, Uchihashi, T, Satoh, T, Kato, K.
Deposit date:2017-08-26
Release date:2018-01-17
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:Conversion of functionally undefined homopentameric protein PbaA into a proteasome activator by mutational modification of its C-terminal segment conformation
Protein Eng. Des. Sel., 31, 2018
5XJE
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BU of 5xje by Molmil
Crystal structure of fucosylated IgG1 Fc complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa
Descriptor: CHLORIDE ION, Immunoglobulin gamma-1 heavy chain, Low affinity immunoglobulin gamma Fc region receptor III-A, ...
Authors:Sakae, Y, Satoh, T, Yagi, H, Yanaka, S, Yamaguchi, T, Isoda, Y, Iida, S, Okamoto, Y, Kato, K.
Deposit date:2017-05-01
Release date:2017-11-01
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fc gamma receptor IIIa.
Sci Rep, 7, 2017
5XJF
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BU of 5xjf by Molmil
Crystal structure of fucosylated IgG Fc Y296W mutant complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ...
Authors:Sakae, Y, Satoh, T, Yagi, H, Yanaka, S, Yamaguchi, T, Isoda, Y, Iida, S, Okamoto, Y, Kato, K.
Deposit date:2017-05-01
Release date:2017-11-01
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fc gamma receptor IIIa.
Sci Rep, 7, 2017
2DGE
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BU of 2dge by Molmil
Crystal structure of oxidized cytochrome C6A from Arabidopsis thaliana
Descriptor: Cytochrome c6, PROTOPORPHYRIN IX CONTAINING FE, ZINC ION
Authors:Chida, H, Yokoyama, T, Kawai, F, Nakazawa, A, Akazaki, H, Takayama, Y, Hirano, T, Suruga, K, Satoh, T, Yamada, S, Kawachi, R, Unzai, S, Nishio, T, Park, S.-Y, Oku, T.
Deposit date:2006-03-11
Release date:2006-07-04
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Crystal structure of oxidized cytochrome c(6A) from Arabidopsis thaliana
Febs Lett., 580, 2006
6KRU
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BU of 6kru by Molmil
Crystal structure of mouse IgG2b Fc
Descriptor: Ig gamma-2B chain C region, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:Taniguchi, Y, Satoh, T, Yagi, H, Kato, K.
Deposit date:2019-08-22
Release date:2020-01-22
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q.
Int J Mol Sci, 21, 2019
6KRV
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BU of 6krv by Molmil
Crystal structure of mouse IgG2b Fc complexed with B domain of Protein A
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Ig gamma-2B chain C region, ...
Authors:Taniguchi, Y, Satoh, T, Yagi, H, Kato, K.
Deposit date:2019-08-22
Release date:2020-01-22
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q.
Int J Mol Sci, 21, 2019
3VR0
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BU of 3vr0 by Molmil
Crystal structure of Pyrococcus furiosus PbaB, an archaeal proteasome activator
Descriptor: GOLD ION, Putative uncharacterized protein
Authors:Kumoi, K, Satoh, T, Hiromoto, T, Mizushima, T, Kamiya, Y, Noda, M, Uchiyama, S, Murata, K, Yagi, H, Kato, K.
Deposit date:2012-04-02
Release date:2013-04-03
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:An archaeal homolog of proteasome assembly factor functions as a proteasome activator
Plos One, 8, 2013
3AUL
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BU of 3aul by Molmil
Crystal structure of wild-type Lys48-linked diubiquitin in an open conformation
Descriptor: Polyubiquitin-C
Authors:Hirano, T, Olivier, S, Yagi, M, Takemoto, E, Hiromoto, T, Satoh, T, Mizushima, T, Kato, K.
Deposit date:2011-02-09
Release date:2011-09-07
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:Conformational dynamics of wild-type Lys48-linked diubiquitin in solution
J.Biol.Chem., 286, 2011
3VQR
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BU of 3vqr by Molmil
Structure of a dye-linked L-proline dehydrogenase mutant from the aerobic hyperthermophilic archaeon, Aeropyrum pernix
Descriptor: 1,2-ETHANEDIOL, ACETATE ION, FLAVIN-ADENINE DINUCLEOTIDE, ...
Authors:Sakuraba, H, Ohshima, T, Satomura, T, Yoneda, K.
Deposit date:2012-03-29
Release date:2012-04-25
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.01 Å)
Cite:Crystal Structure of Novel Dye-linked L-Proline Dehydrogenase from Hyperthermophilic Archaeon Aeropyrum pernix
J.Biol.Chem., 287, 2012
3WV0
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BU of 3wv0 by Molmil
O-glycan attached to herpes simplex virus type 1 glycoprotein gB is recognized by the Ig V-set domain of human paired immunoglobulin-like type 2 receptor alpha
Descriptor: Envelope glycoprotein B, N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-galactopyranose, Paired immunoglobulin-like type 2 receptor alpha, ...
Authors:Kuroki, K, Wang, J, Ose, T, Yamaguchi, M, Tabata, S, Maita, N, Nakamura, S, Kajikawa, M, Kogure, A, Satoh, T, Arase, H, Maenaka, K.
Deposit date:2014-05-10
Release date:2014-06-11
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural basis for simultaneous recognition of an O-glycan and its attached peptide of mucin family by immune receptor PILR alpha
Proc.Natl.Acad.Sci.USA, 111, 2014
3WUZ
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BU of 3wuz by Molmil
Crystal structure of the Ig V-set domain of human paired immunoglobulin-like type 2 receptor alpha
Descriptor: CITRIC ACID, ISOPROPYL ALCOHOL, Paired immunoglobulin-like type 2 receptor alpha
Authors:Kuroki, K, Wang, J, Ose, T, Yamaguchi, M, Tabata, S, Maita, N, Nakamura, S, Kajikawa, M, Kogure, A, Satoh, T, Arase, H, Maenaka, K.
Deposit date:2014-05-10
Release date:2014-06-11
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:Structural basis for simultaneous recognition of an O-glycan and its attached peptide of mucin family by immune receptor PILR alpha
Proc.Natl.Acad.Sci.USA, 111, 2014

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