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PDB: 121 results

8XJ0
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BU of 8xj0 by Molmil
Crystal structure of AmFab mutant - P40C/E165C (Light chain), G10C/P210C(Heavy chain)
Descriptor: Adalimumab Fab Heavy chain, Adalimumab Fab Light chain
Authors:Senda, M, Yoshikawa, M, Nakamura, H, Ohkuri, T, Senda, T.
Deposit date:2023-12-20
Release date:2024-02-14
Last modified:2024-10-30
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Stabilization of adalimumab Fab through the introduction of disulfide bonds between the variable and constant domains.
Biochem.Biophys.Res.Commun., 700, 2024
2E4P
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BU of 2e4p by Molmil
Crystal structure of BphA3 (oxidized form)
Descriptor: Biphenyl dioxygenase ferredoxin subunit, FE2/S2 (INORGANIC) CLUSTER, SULFATE ION, ...
Authors:Senda, M, Kishigami, S, Kimura, S, Ishida, T, Fukuda, M, Senda, T.
Deposit date:2006-12-15
Release date:2007-10-16
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2 Å)
Cite:Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin
J.Mol.Biol., 373, 2007
2E4Q
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BU of 2e4q by Molmil
Crystal structure of BphA3 (reduced form)
Descriptor: Biphenyl dioxygenase ferredoxin subunit, FE2/S2 (INORGANIC) CLUSTER
Authors:Senda, M, Kishigami, S, Kimura, S, Ishida, T, Fukuda, M, Senda, T.
Deposit date:2006-12-15
Release date:2007-10-16
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin
J.Mol.Biol., 373, 2007
7VHC
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BU of 7vhc by Molmil
Crystal structure of the STX2a complexed with AR4A peptide
Descriptor: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE, Shiga toxin 2 B subunit, inhibitor peptide, ...
Authors:Senda, M, Takahashi, M, Nishikawa, K, Senda, T.
Deposit date:2021-09-22
Release date:2022-07-20
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin.
Sci Rep, 12, 2022
7VHF
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BU of 7vhf by Molmil
Crystal structure of the STX2a complexed with RRA peptide
Descriptor: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE, GLYCEROL, RRA peptide, ...
Authors:Senda, M, Takahashi, M, Nishikawa, K, Senda, T.
Deposit date:2021-09-22
Release date:2022-07-20
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin.
Sci Rep, 12, 2022
7VHE
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BU of 7vhe by Molmil
Crystal structure of the STX2a complexed with RRRA peptide
Descriptor: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE, GLYCEROL, RRRA peptide, ...
Authors:Senda, M, Takahashi, M, Nishikawa, K, Senda, T.
Deposit date:2021-09-22
Release date:2022-07-20
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin.
Sci Rep, 12, 2022
7VHD
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BU of 7vhd by Molmil
Crystal structure of the STX2a complexed with R4A peptide
Descriptor: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE, ARG-ARG-ARG-ARG-ALA, Shiga toxin 2 B subunit, ...
Authors:Senda, M, Takahashi, M, Nishikawa, K, Senda, T.
Deposit date:2021-09-22
Release date:2022-07-20
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin.
Sci Rep, 12, 2022
7DNN
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BU of 7dnn by Molmil
Crystal structure of the AgCarB2-C2 complex with homoorientin
Descriptor: 2-[3,4-bis(oxidanyl)phenyl]-6-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one, AP_endonuc_2 domain-containing protein, AgCarC2, ...
Authors:Senda, M, Kumano, T, Watanabe, S, Kobayashi, M, Senda, T.
Deposit date:2020-12-10
Release date:2021-10-20
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Structural basis for the metabolism of xenobiotic C-glycosides by intestinal bacteria
Nat Commun, 2021
7DNM
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BU of 7dnm by Molmil
Crystal structure of the AgCarB2-C2 complex
Descriptor: AP_endonuc_2 domain-containing protein, AgCarC2, IODIDE ION, ...
Authors:Senda, M, Kumano, T, Watanabe, S, Kobayashi, M, Senda, T.
Deposit date:2020-12-10
Release date:2021-10-20
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural basis for the metabolism of xenobiotic C-glycosides by intestinal bacteria
Nat Commun, 2021
7DVE
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BU of 7dve by Molmil
Crystal structure of FAD-dependent C-glycoside oxidase
Descriptor: 6'''-hydroxyparomomycin C oxidase, FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION
Authors:Senda, M, Watanabe, S, Kumano, T, Kobayashi, M, Senda, T.
Deposit date:2021-01-13
Release date:2021-09-08
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:FAD-dependent C -glycoside-metabolizing enzymes in microorganisms: Screening, characterization, and crystal structure analysis.
Proc.Natl.Acad.Sci.USA, 118, 2021
7EM5
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BU of 7em5 by Molmil
Crystal structure of the PI5P4Kbeta F205L-XTP complex
Descriptor: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Authors:Senda, M, Senda, T.
Deposit date:2021-04-13
Release date:2022-03-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
7EM1
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BU of 7em1 by Molmil
Crystal structure of the PI5P4Kbeta-ITP complex
Descriptor: INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Authors:Senda, M, Senda, T.
Deposit date:2021-04-13
Release date:2022-03-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.65 Å)
Cite:The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
7EM6
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BU of 7em6 by Molmil
Crystal structure of the PI5P4Kbeta N203D-ITP complex
Descriptor: INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Authors:Senda, M, Senda, T.
Deposit date:2021-04-13
Release date:2022-03-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.95 Å)
Cite:The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
7EM7
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BU of 7em7 by Molmil
Crystal structure of the PI5P4Kbeta N203D-XTP complex
Descriptor: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Authors:Senda, M, Senda, T.
Deposit date:2021-04-13
Release date:2022-03-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.45 Å)
Cite:The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
7EM3
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BU of 7em3 by Molmil
Crystal structure of the PI5P4Kbeta-2a-ATP complex
Descriptor: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Authors:Senda, M, Senda, T.
Deposit date:2021-04-13
Release date:2022-03-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
7EM4
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BU of 7em4 by Molmil
Crystal structure of the PI5P4Kbeta F205L-ITP complex
Descriptor: INOSINE-5'-DIPHOSPHATE, Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Authors:Senda, M, Senda, T.
Deposit date:2021-04-13
Release date:2022-03-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
7EM8
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BU of 7em8 by Molmil
Crystal structure of the PI5P4Kbeta T201M-2a-ATP complex
Descriptor: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Authors:Senda, M, Senda, T.
Deposit date:2021-04-13
Release date:2022-03-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.05 Å)
Cite:The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
7EM2
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BU of 7em2 by Molmil
Crystal structure of the PI5P4Kbeta-XTP complex
Descriptor: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta, [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate, [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Authors:Senda, M, Senda, T.
Deposit date:2021-04-13
Release date:2022-03-30
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Structure, 30, 2022
7E18
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BU of 7e18 by Molmil
Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor YH-53
Descriptor: 1,2-ETHANEDIOL, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, Replicase polyprotein 1ab
Authors:Senda, M, Konno, S, Hayashi, Y, Senda, T.
Deposit date:2021-02-01
Release date:2021-06-23
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
J.Med.Chem., 65, 2022
7E19
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BU of 7e19 by Molmil
Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor SH-5
Descriptor: (phenylmethyl) N-[(2S)-1-[[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-methyl-1-oxidanylidene-butan-2-yl]carbamate, 3C-like proteinase
Authors:Senda, M, Konno, S, Hayashi, Y, Senda, T.
Deposit date:2021-02-01
Release date:2021-06-23
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
J.Med.Chem., 65, 2022
7C5W
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BU of 7c5w by Molmil
Crystal structure of the iota-carbonic anhydrase from cyanobacterium complexed with iodide
Descriptor: IODIDE ION, iota-carbonic anhydrase
Authors:Senda, M, Senda, T.
Deposit date:2020-05-20
Release date:2021-04-28
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Characterization of a novel type of carbonic anhydrase that acts without metal cofactors.
Bmc Biol., 19, 2021
7C5V
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BU of 7c5v by Molmil
Crystal structure of the iota-carbonic anhydrase from cyanobacterium complexed with bicarbonate
Descriptor: BICARBONATE ION, iota-carbonic anhydrase
Authors:Senda, M, Senda, T.
Deposit date:2020-05-20
Release date:2021-04-28
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.65 Å)
Cite:Characterization of a novel type of carbonic anhydrase that acts without metal cofactors.
Bmc Biol., 19, 2021
7C5Y
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BU of 7c5y by Molmil
Crystal structure of the iota-carbonic anhydrase from eukaryotic microalga complexed with iodide
Descriptor: IODIDE ION, iota-carbonic anhydrase
Authors:Senda, M, Senda, T.
Deposit date:2020-05-20
Release date:2021-04-28
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Characterization of a novel type of carbonic anhydrase that acts without metal cofactors.
Bmc Biol., 19, 2021
7C5X
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BU of 7c5x by Molmil
Crystal structure of the iota-carbonic anhydrase from eukaryotic microalga complexed with bicarbonate
Descriptor: BICARBONATE ION, iota-carbonic anhydrase
Authors:Senda, M, Senda, T.
Deposit date:2020-05-20
Release date:2021-04-28
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:Characterization of a novel type of carbonic anhydrase that acts without metal cofactors.
Bmc Biol., 19, 2021
7D98
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BU of 7d98 by Molmil
Crystal structure of full-length CbnR complexed with the target DNA complex
Descriptor: DNA (56-mer), LysR-type regulatory protein
Authors:Senda, M, Giannopoulou, E, Senda, T.
Deposit date:2020-10-12
Release date:2021-03-10
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.6 Å)
Cite:Crystal structure of the full-length LysR-type transcription regulator CbnR in complex with promoter DNA.
Febs J., 288, 2021

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PDB entries from 2024-10-30

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