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7X7O
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BU of 7x7o by Molmil
SARS-CoV-2 spike RBD in complex with neutralizing antibody UT28K
Descriptor: Spike protein S1, UT28K Fab, heavy chain, ...
Authors:Ozawa, T, Tani, H, Anraku, Y, Kita, S, Igarashi, E, Saga, Y, Inasaki, N, Kawasuji, H, Yamada, H, Sasaki, S, Somekawa, M, Sasaki, J, Hayakawa, Y, Yamamoto, Y, Morinaga, Y, Kurosawa, N, Isobe, M, Fukuhara, H, Maenaka, K, Hashiguchi, T, Kishi, H, Kitajima, I, Saito, S, Niimi, H.
Deposit date:2022-03-10
Release date:2022-05-25
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.75 Å)
Cite:Novel super-neutralizing antibody UT28K is capable of protecting against infection from a wide variety of SARS-CoV-2 variants.
Mabs, 14, 2022
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
7YH7
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BU of 7yh7 by Molmil
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
8JYM
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BU of 8jym by Molmil
Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed 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, Spike glycoprotein
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Sasaki, J, Sasaki-Tabata, K, Maenaka, K, Hashiguchi, T.
Deposit date:2023-07-03
Release date:2024-01-03
Method:ELECTRON MICROSCOPY (2.79 Å)
Cite:Virological characteristics of the SARS-CoV-2 XBB.1.5 variant
To Be Published
8JYK
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BU of 8jyk by Molmil
Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 1)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Sasaki, J, Sasaki-Tabata, K, Maenaka, K, Hashiguchi, T.
Deposit date:2023-07-03
Release date:2024-01-03
Method:ELECTRON MICROSCOPY (2.59 Å)
Cite:Virological characteristics of the SARS-CoV-2 XBB.1.5 variant
To Be Published
8JYP
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BU of 8jyp by Molmil
Structure of SARS-CoV-2 XBB.1.5 spike RBD in complex with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Sasaki, J, Sasaki-Tabata, K, Maenaka, K, Hashiguchi, T.
Deposit date:2023-07-03
Release date:2024-01-03
Method:ELECTRON MICROSCOPY (3.38 Å)
Cite:Virological characteristics of the SARS-CoV-2 XBB.1.5 variant
To Be Published
8JYN
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BU of 8jyn by Molmil
Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (1-up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Sasaki, J, Sasaki-Tabata, K, Maenaka, K, Hashiguchi, T.
Deposit date:2023-07-03
Release date:2024-01-03
Method:ELECTRON MICROSCOPY (3.04 Å)
Cite:Virological characteristics of the SARS-CoV-2 XBB.1.5 variant
To Be Published
8JYO
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BU of 8jyo by Molmil
Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (2-up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Sasaki, J, Sasaki-Tabata, K, Maenaka, K, Hashiguchi, T.
Deposit date:2023-07-03
Release date:2024-01-03
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Virological characteristics of the SARS-CoV-2 XBB.1.5 variant
To Be Published
8K5H
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BU of 8k5h by Molmil
Structure of the SARS-CoV-2 BA.1 spike with UT28-RD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Chen, L, Kita, S, Anraku, Y, Maenaka, K.
Deposit date:2023-07-21
Release date:2023-12-27
Method:ELECTRON MICROSCOPY (3.22 Å)
Cite:In silico-designed UT28K with two amino acid substitutions is capable of neutralization of resistant SARS-CoV2 Omicrons BA.1 valiant.
To Be Published
8K5G
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BU of 8k5g by Molmil
Structure of the SARS-CoV-2 BA.1 RBD with UT28-RD
Descriptor: Spike protein S1, UT28K-RD Fab Heavy chain, UT28K-RD Fab Light chain
Authors:Chen, L, Kita, S, Anraku, Y, Maenaka, K.
Deposit date:2023-07-21
Release date:2023-12-27
Method:ELECTRON MICROSCOPY (3.41 Å)
Cite:In silico-designed UT28K with two amino acid substitutions is capable of neutralization of resistant SARS-CoV2 Omicrons BA.1 valiant.
To Be Published
7XBD
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BU of 7xbd by Molmil
Cryo-EM structure of human galanin receptor 2
Descriptor: Galanin, Galanin receptor type 2, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, ...
Authors:Ishimoto, N, Kita, S, Park, S.Y.
Deposit date:2022-03-21
Release date:2022-07-13
Last modified:2022-08-10
Method:ELECTRON MICROSCOPY (3.11 Å)
Cite:Structure of the human galanin receptor 2 bound to galanin and Gq reveals the basis of ligand specificity and how binding affects the G-protein interface.
Plos Biol., 20, 2022
6K6N
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BU of 6k6n by Molmil
Crystal structure of SIVmac239 Nef protein
Descriptor: Protein Nef
Authors:Hirao, K, Andrews, S, Kuroki, K, Kusaka, H, Tadokoro, T, Kita, S, Ose, T, Rowland-Jones, S, Maenaka, K.
Deposit date:2019-06-04
Release date:2020-03-25
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.0002 Å)
Cite:Structure of HIV-2 Nef Reveals Features Distinct from HIV-1 Involved in Immune Regulation.
Iscience, 23, 2020
6K6M
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BU of 6k6m by Molmil
Crystal structure of HIV-2 Nef protein
Descriptor: Protein Nef
Authors:Hirao, K, Andrews, S, Kuroki, K, Kusaka, H, Tadokoro, T, Kita, S, Ose, T, Rowland-Jones, S, Maenaka, K.
Deposit date:2019-06-04
Release date:2020-03-25
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.072 Å)
Cite:Structure of HIV-2 Nef Reveals Features Distinct from HIV-1 Involved in Immune Regulation.
Iscience, 23, 2020
6K60
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BU of 6k60 by Molmil
Structural and functional basis for HLA-G isoform recognition of immune checkpoint receptor LILRBs
Descriptor: Beta-2-microglobulin, HLA class I histocompatibility antigen, alpha chain G, ...
Authors:Kuroki, K, Matsubara, H, Kanda, R, Miyashita, N, Shiroishi, M, Fukunaga, Y, Kamishikiryo, J, Fukunaga, A, Hirose, K, Sugita, Y, Kita, S, Ose, T, Maenaka, K.
Deposit date:2019-05-31
Release date:2019-11-27
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (3.149 Å)
Cite:Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms.
J Immunol., 203, 2019
4W96
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BU of 4w96 by Molmil
Crystal structure of cross-linked tetragonal hen egg white lysozyme soaked with 5mM [Ru(CO)3Cl2]2 followed by the reaction in deoxy-myoglobin solution
Descriptor: CHLORIDE ION, DIMETHYLFORMAMIDE, Lysozyme C, ...
Authors:Tabe, H, Fujita, K, Abe, S, Tsujimoto, M, Kuchimaru, T, Kizaka-Kondo, S, Takano, M, Kitagawa, S, Ueno, T.
Deposit date:2014-08-27
Release date:2014-12-31
Last modified:2020-01-29
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Preparation of a Cross-Linked Porous Protein Crystal Containing Ru Carbonyl Complexes as a CO-Releasing Extracellular Scaffold
Inorg.Chem., 54, 2015
1J19
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BU of 1j19 by Molmil
Crystal structure of the radxin FERM domain complexed with the ICAM-2 cytoplasmic peptide
Descriptor: 16-mer peptide from Intercellular adhesion molecule-2, radixin
Authors:Hamada, K, Shimizu, T, Yonemura, S, Tsukita, S, Tsukita, S, Hakoshima, T.
Deposit date:2002-12-02
Release date:2003-03-11
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structural basis of adhesion-molecule recognition by ERM proteins revealed by the crystal structure of the radixin-ICAM-2 complex
EMBO J., 22, 2003
4W94
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BU of 4w94 by Molmil
Crystal structure of cross-linked tetragonal hen egg white lysozyme soaked with 5mM [Ru(CO)3Cl2]2
Descriptor: CHLORIDE ION, DIMETHYLFORMAMIDE, Lysozyme C, ...
Authors:Tabe, H, Fujita, K, Abe, S, Tsujimoto, M, Kuchimaru, T, Kizaka-Kondo, S, Takano, M, Kitagawa, S, Ueno, T.
Deposit date:2014-08-27
Release date:2014-12-31
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Preparation of a Cross-Linked Porous Protein Crystal Containing Ru Carbonyl Complexes as a CO-Releasing Extracellular Scaffold
Inorg.Chem., 54, 2015
3WNL
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BU of 3wnl by Molmil
D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltohexaose
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CALCIUM ION, Cycloisomaltooligosaccharide glucanotransferase, ...
Authors:Suzuki, N, Fujimoto, Z, Kim, Y.M, Momma, M, Kishine, N, Suzuki, R, Suzuki, S, Kitamura, S, Kobayashi, M, Kimura, A, Funane, K.
Deposit date:2013-12-10
Release date:2014-02-05
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural elucidation of the cyclization mechanism of alpha-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase.
J.Biol.Chem., 289, 2014
3W6A
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BU of 3w6a by Molmil
Crystal structure of cross-linked tetragonal hen egg white lysozyme soaked wiht 5mM [Ru(benzene)Cl2]2
Descriptor: ACETATE ION, Benzeneruthenium(II) chloride, CHLORIDE ION, ...
Authors:Tabe, H, Abe, S, Hikage, T, Kitagawa, S, Ueno, T.
Deposit date:2013-02-13
Release date:2014-02-19
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:Solid Artificial Metalloenzymes: Post-Engineering of Porous Protein Crystals by Organometallic Complexes
To be Published
6YAA
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BU of 6yaa by Molmil
Structure of the (SR) Ca2+-ATPase bound to the inhibitor compound CAD204520 and TNP-ATP
Descriptor: 4-[2-[(2~{R})-2-[3-propyl-6-(trifluoromethyloxy)-1~{H}-indol-2-yl]piperidin-1-yl]ethyl]morpholine, POTASSIUM ION, SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE, ...
Authors:Heit, S, Marchesini, M, Gherli, A, Montanaro, A, Patrizi, L, Sorrentino, C, Pagliaro, L, Rompietti, C, Kitara, S, Olesen, C.E, Moller, J.V, Savi, M, Bocchi, L, Vilella, R, Rizzi, F, Baglione, M, Rastelli, G, Loiacona, C, La Starza, R, Mecucci, C, Stegmair, K, Aversa, F, Stilli, D, Lund Winther, A.M, Sportoletti, P, Dalby-Brown, W, Roti, G, Bublitz, M.
Deposit date:2020-03-11
Release date:2020-05-20
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (3.4 Å)
Cite:Blockade of Oncogenic NOTCH1 with the SERCA Inhibitor CAD204520 in T Cell Acute Lymphoblastic Leukemia.
Cell Chem Biol, 27, 2020
1GC7
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BU of 1gc7 by Molmil
CRYSTAL STRUCTURE OF THE RADIXIN FERM DOMAIN
Descriptor: RADIXIN
Authors:Hamada, K, Shimizu, T, Matsui, T, Tsukita, S, Tsukita, S, Hakoshima, T.
Deposit date:2000-07-21
Release date:2000-09-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain.
EMBO J., 19, 2000
1GC6
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BU of 1gc6 by Molmil
CRYSTAL STRUCTURE OF THE RADIXIN FERM DOMAIN COMPLEXED WITH INOSITOL-(1,4,5)-TRIPHOSPHATE
Descriptor: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE, RADIXIN
Authors:Hamada, K, Shimizu, T, Matsui, T, Tsukita, S, Tsukita, S, Hakoshima, T.
Deposit date:2000-07-21
Release date:2000-09-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain.
EMBO J., 19, 2000
3WNP
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BU of 3wnp by Molmil
D308A, F268V, D469Y, A513V, and Y515S quintuple mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltoundecaose
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CALCIUM ION, Cycloisomaltooligosaccharide glucanotransferase, ...
Authors:Suzuki, R, Suzuki, N, Fujimoto, Z, Momma, M, Kimura, K, Kitamura, S, Kimura, A, Funane, K.
Deposit date:2013-12-10
Release date:2014-02-05
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Molecular engineering of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040: structural determinants for the reaction product size and reactivity.
Biochem.J., 467, 2015
6E69
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BU of 6e69 by Molmil
Ortho-substituted phenyl sulfonyl fluoride and fluorosulfate as potent elastase inhibitory fragments
Descriptor: 2-(fluorosulfonyl)benzene-1-sulfonic acid, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Wolan, D.W, Woehl, J.L, Kitamura, S.
Deposit date:2018-07-24
Release date:2019-07-24
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.33 Å)
Cite:SuFEx-enabled, agnostic discovery of covalent inhibitors of human neutrophil elastase.
Proc.Natl.Acad.Sci.USA, 116, 2019
1ISN
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BU of 1isn by Molmil
Crystal structure of merlin FERM domain
Descriptor: merlin
Authors:Shimizu, T, Seto, A, Maita, N, Hamada, K, Tsukita, S, Tsukita, S, Hakoshima, T.
Deposit date:2001-12-13
Release date:2002-04-03
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structural basis for neurofibromatosis type 2. Crystal structure of the merlin FERM domain.
J.Biol.Chem., 277, 2002

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