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PDB: 772 results

3WOC
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Crystal structure of a prostate-specific WGA16 glycoprotein lectin, form II
Descriptor: 1,4-DIETHYLENE DIOXIDE, GLYCEROL, SULFATE ION, ...
Authors:Garenaux, E, Kanagawa, M, Tsuchiyama, T, Hori, K, Kanazawa, T, Goshima, A, Chiba, M, Yasue, H, Ikeda, A, Yamaguchi, Y, Sato, C, Kitajima, K.
Deposit date:2013-12-26
Release date:2014-12-31
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Discovery, Primary, and Crystal Structures and Capacitation-related Properties of a Prostate-derived Heparin-binding Protein WGA16 from Boar Sperm
J.Biol.Chem., 290, 2015
3WOB
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Crystal structure of a prostate-specific WGA16 glycoprotein lectin, form I
Descriptor: hypothetical protein
Authors:Garenaux, E, Kanagawa, M, Tsuchiyama, T, Hori, K, Kanazawa, T, Goshima, A, Chiba, M, Yasue, H, Ikeda, A, Yamaguchi, Y, Sato, C, Kitajima, K.
Deposit date:2013-12-26
Release date:2014-12-31
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Discovery, Primary, and Crystal Structures and Capacitation-related Properties of a Prostate-derived Heparin-binding Protein WGA16 from Boar Sperm
J.Biol.Chem., 290, 2015
7YH7
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SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, ...
Authors:Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y.
Deposit date:2022-07-13
Release date:2023-07-19
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
3VPE
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Crystal Structure of Metallo-beta-Lactamase SMB-1
Descriptor: ACETATE ION, GLYCEROL, Metallo-beta-lactamase, ...
Authors:Wachino, J, Yamaguchi, Y, Mori, S, Arakawa, Y, Shibayama, K.
Deposit date:2012-02-29
Release date:2013-02-13
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural Insights into the Subclass B3 Metallo-beta-Lactamase SMB-1 and the Mode of Inhibition by the Common Metallo- -Lactamase Inhibitor Mercaptoacetate
Antimicrob.Agents Chemother., 57, 2013
3VQZ
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Crystal structure of metallo-beta-lactamase, SMB-1, in a complex with mercaptoacetic acid
Descriptor: Metallo-beta-lactamase, SODIUM ION, SULFANYLACETIC ACID, ...
Authors:Wachino, J, Yamaguchi, Y, Mori, S, Arakawa, Y, Shibayama, K.
Deposit date:2012-04-02
Release date:2013-02-13
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural Insights into the Subclass B3 Metallo-beta-Lactamase SMB-1 and the Mode of Inhibition by the Common Metallo- -Lactamase Inhibitor Mercaptoacetate
Antimicrob.Agents Chemother., 57, 2013
7YH6
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BU of 7yh6 by Molmil
Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-8
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, NIV-8 Fab light chain, ...
Authors:Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y.
Deposit date:2022-07-12
Release date:2023-07-19
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
8HGM
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Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-11 Fab heavy chain, NIV-11 Fab light chain, ...
Authors:Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y.
Deposit date:2022-11-15
Release date:2023-10-25
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
8HGL
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SARS-CoV-2 spike in complex with neutralizing antibody NIV-11
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-11 Fab heavy chain, ...
Authors:Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y.
Deposit date:2022-11-15
Release date:2023-10-25
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
8HES
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BU of 8hes by Molmil
Crystal structure of SARS-CoV-2 RBD and NIV-10 complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-10 Fab H-chain, NIV-10 Fab L-chain, ...
Authors:Moriyama, S, Anraku, Y, Taminishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y.
Deposit date:2022-11-08
Release date:2023-11-08
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
1WYW
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BU of 1wyw by Molmil
Crystal Structure of SUMO1-conjugated thymine DNA glycosylase
Descriptor: CHLORIDE ION, G/T mismatch-specific thymine DNA glycosylase, MAGNESIUM ION, ...
Authors:Baba, D, Maita, N, Jee, J.G, Uchimura, Y, Saitoh, H, Sugasawa, K, Hanaoka, F, Tochio, H, Hiroaki, H, Shirakawa, M.
Deposit date:2005-02-17
Release date:2005-06-21
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal structure of thymine DNA glycosylase conjugated to SUMO-1.
Nature, 435, 2005
3VZE
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BU of 3vze by Molmil
Crystal structure of human pancreatic secretory protein ZG16p with alpha1,3-mannobiose
Descriptor: CHLORIDE ION, Zymogen granule membrane protein 16, alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose
Authors:Kanagawa, M, Yamaguchi, Y.
Deposit date:2012-10-11
Release date:2013-10-16
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin
J.Biol.Chem., 289, 2014
3VY6
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Crystal structure of human pancreatic secretory protein ZG16p with laminaribiose
Descriptor: CHLORIDE ION, Zymogen granule membrane protein 16, beta-D-glucopyranose-(1-3)-beta-D-glucopyranose
Authors:Kanagawa, M, Yamaguchi, Y.
Deposit date:2012-09-21
Release date:2013-09-25
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin
J.Biol.Chem., 289, 2014
3VZF
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BU of 3vzf by Molmil
Crystal structure of human pancreatic secretory protein ZG16p with methyl alpha-D-mannopyranoside
Descriptor: CHLORIDE ION, Zymogen granule membrane protein 16, methyl alpha-D-mannopyranoside
Authors:Kanagawa, M, Yamaguchi, Y.
Deposit date:2012-10-11
Release date:2013-10-16
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Structural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin
J.Biol.Chem., 289, 2014
3VY7
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Crystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-serine
Descriptor: CHLORIDE ION, SERINE, Zymogen granule membrane protein 16, ...
Authors:Kanagawa, M, Yamaguchi, Y.
Deposit date:2012-09-21
Release date:2013-09-25
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.14 Å)
Cite:Structural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin
J.Biol.Chem., 289, 2014
3VZG
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BU of 3vzg by Molmil
Crystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-threonine
Descriptor: CHLORIDE ION, THREONINE, Zymogen granule membrane protein 16, ...
Authors:Kanagawa, M, Yamaguchi, Y.
Deposit date:2012-10-11
Release date:2013-10-16
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin
J.Biol.Chem., 289, 2014
8FD4
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BU of 8fd4 by Molmil
Solution structure of mu-theraphotoxin Cg4a from Chinese tarantula Chilobrachys jingzhao
Descriptor: Jingzhaotoxin F7-10.36
Authors:Sharma, G, Jia, X, Chin, Y.K.Y, Mobli, M.
Deposit date:2022-12-01
Release date:2023-11-08
Method:SOLUTION NMR
Cite:Solution structure of mu-theraphotoxin Cg4a from Chinese tarantula Chilobrachys jingzhao
To Be Published
5FNN
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BU of 5fnn by Molmil
Iron and Selenomethionine containing Iron sulfur cluster repair protein YtfE
Descriptor: CHLORIDE ION, FE (II) ION, FE (III) ION, ...
Authors:Lo, F.-C, Hsieh, C.-C, Maestre-Reyna, M, Chen, C.-Y, Ko, T.-P, Horng, Y.-C, Lai, Y.-C, Chiang, Y.-W, Chou, C.-M, Chiang, C.-H, Huang, W.-N, Liaw, W.-F.
Deposit date:2015-11-16
Release date:2016-04-27
Last modified:2017-07-12
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:Crystal Structure of the Repair of Iron Centers Protein Ytfe and its Interaction with No
Chemistry, 22, 2016
4XRE
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BU of 4xre by Molmil
Crystal structure of Gnk2 complexed with mannose
Descriptor: Antifungal protein ginkbilobin-2, alpha-D-mannopyranose
Authors:Miyakawa, T, Hatano, K, Miyauchi, Y, Suwa, Y, Sawano, Y, Tanokura, M.
Deposit date:2015-01-21
Release date:2015-02-25
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.597 Å)
Cite:A secreted protein with plant-specific cysteine-rich motif functions as a mannose-binding lectin that exhibits antifungal activity.
Plant Physiol., 166, 2014
5FNY
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BU of 5fny by Molmil
Low solvent content crystal form of Zn containing Iron sulfur cluster repair protein YtfE
Descriptor: FE (III) ION, IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE, NONAETHYLENE GLYCOL, ...
Authors:Lo, F.-C, Hsieh, C.-C, Maestre-Reyna, M, Chen, C.-Y, Ko, T.-P, Horng, Y.-C, Lai, Y.-C, Chiang, Y.-W, Chou, C.-M, Chiang, C.-H, Huang, W.-N, Liaw, W.-F.
Deposit date:2015-11-17
Release date:2016-04-27
Last modified:2024-01-10
Method:X-RAY DIFFRACTION (2.01 Å)
Cite:Crystal Structure of the Repair of Iron Centers Protein Ytfe and its Interaction with No
Chemistry, 22, 2016
5FNP
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High resolution Zn containing Iron sulfur cluster repair protein YtfE
Descriptor: CHLORIDE ION, IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE, OXYGEN ATOM, ...
Authors:Lo, F.-C, Hsieh, C.-C, Maestre-Reyna, M, Chen, C.-Y, Ko, T.-P, Horng, Y.-C, Lai, Y.-C, Chiang, Y.-W, Chou, C.-M, Chiang, C.-H, Huang, W.-N, Liaw, W.-F.
Deposit date:2015-11-16
Release date:2016-04-27
Last modified:2024-01-10
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal Structure of the Repair of Iron Centers Protein Ytfe and its Interaction with No
Chemistry, 22, 2016
4YSV
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BU of 4ysv by Molmil
Structure of aminoacid racemase in apo-form
Descriptor: Putative 4-aminobutyrate aminotransferase
Authors:Sakuraba, H, Mutaguchi, Y, Hayashi, J, Ohshima, T.
Deposit date:2015-03-17
Release date:2016-04-20
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.77 Å)
Cite:Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri.
Acta Crystallogr D Struct Biol, 73, 2017
6A8V
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PhoQ sensor domain (D179R mutant): analysis of internal cavity
Descriptor: Sensor protein PhoQ
Authors:Yoshitani, K, Ishii, E, Taniguchi, K, Sugimoto, H, Shiro, Y, Mori, H, Akiyama, Y, Kato, A, Utsumi, R, Eguchi, Y.
Deposit date:2018-07-10
Release date:2019-01-30
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Identification of an internal cavity in the PhoQ sensor domain for PhoQ activity and SafA-mediated control.
Biosci. Biotechnol. Biochem., 83, 2019
6A8U
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BU of 6a8u by Molmil
PhoQ sensor domain (wild type): analysis of internal cavity
Descriptor: Sensor protein PhoQ
Authors:Yoshitani, K, Ishii, E, Taniguchi, K, Sugimoto, H, Shiro, Y, Mori, H, Akiyama, Y, Kato, A, Utsumi, R, Eguchi, Y.
Deposit date:2018-07-10
Release date:2019-01-30
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.848 Å)
Cite:Identification of an internal cavity in the PhoQ sensor domain for PhoQ activity and SafA-mediated control.
Biosci. Biotechnol. Biochem., 83, 2019
3W1W
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Protein-drug complex
Descriptor: 1,2-ETHANEDIOL, 2-HYDROXYBENZOIC ACID, CHOLIC ACID, ...
Authors:Ishii, R, Gupta, V, Yamaguchi, Y, Handa, H, Nureki, O.
Deposit date:2012-11-21
Release date:2013-10-09
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.006 Å)
Cite:Salicylic Acid induces mitochondrial injury by inhibiting ferrochelatase heme biosynthesis activity
Mol.Pharmacol., 84, 2013
3WBQ
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Crystal structure of carbohydrate recognition domain of Blood Dendritic Cell Antigen-2 (BDCA2) lectin (crystal form-2)
Descriptor: C-type lectin domain family 4 member C
Authors:Nagae, M, Ikeda, A, Kitago, Y, Matsumoto, N, Yamamoto, K, Yamaguchi, Y.
Deposit date:2013-05-20
Release date:2013-12-25
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer.
Proteins, 82, 2014

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