4Z9Y
| Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Pectobacterium carotovorum | Descriptor: | 2-deoxy-D-gluconate 3-dehydrogenase, SULFATE ION | Authors: | Takase, R, Maruyama, Y, Oiki, S, Mikami, B, Murata, K, Hashimoto, W. | Deposit date: | 2015-04-13 | Release date: | 2015-04-29 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.63 Å) | Cite: | Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity Proteins, 84, 2016
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4ZA2
| Crystal structure of Pectobacterium carotovorum 2-keto-3-deoxy-D-gluconate dehydrogenase complexed with NAD+ | Descriptor: | 2-deoxy-D-gluconate 3-dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | Authors: | Takase, R, Maruyama, Y, Oiki, S, Mikami, B, Murata, K, Hashimoto, W. | Deposit date: | 2015-04-13 | Release date: | 2015-04-29 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity Proteins, 84, 2016
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4E1Y
| Alginate lyase A1-III H192A apo form | Descriptor: | Alginate lyase | Authors: | Mikami, B, Ban, M, Suzuki, S, Yoon, H.-J, Miyake, O, Yamasaki, M, Ogura, K, Maruyama, Y, Hashimoto, W, Murata, K. | Deposit date: | 2012-03-07 | Release date: | 2012-04-11 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III Acta Crystallogr.,Sect.D, 68, 2012
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8XBH
| Human GPR34 -Gi complex bound to M1 | Descriptor: | (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, ... | Authors: | Kawahara, R, Shihoya, W, Nureki, O. | Deposit date: | 2023-12-06 | Release date: | 2023-12-27 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (2.83 Å) | Cite: | Structural basis for lysophosphatidylserine recognition by GPR34. Nat Commun, 15, 2024
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8XBG
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8XBE
| Human GPR34 -Gi complex bound to S3E-LysoPS | Descriptor: | (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[(~{Z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, ... | Authors: | Kawahara, R, Shihoya, W, Nureki, O. | Deposit date: | 2023-12-06 | Release date: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Structural basis for lysophosphatidylserine recognition by GPR34. Nat Commun, 15, 2024
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8XBI
| Human GPR34 -Gi complex bound to M1, receptor focused | Descriptor: | (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid, Probable G-protein coupled receptor 34 | Authors: | Kawahara, R, Shihoya, W, Nureki, O. | Deposit date: | 2023-12-06 | Release date: | 2023-12-27 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.06 Å) | Cite: | Structural basis for lysophosphatidylserine recognition by GPR34. Nat Commun, 15, 2024
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3IM0
| Crystal structure of Chlorella virus vAL-1 soaked in 200mM D-glucuronic acid, 10% PEG-3350, and 200mM glycine-NaOH (pH 10.0) | Descriptor: | VAL-1, beta-D-glucopyranuronic acid | Authors: | Ogura, K, Yamasaki, M, Hashidume, T, Yamada, T, Mikami, B, Hashimoto, W, Murata, K. | Deposit date: | 2009-08-08 | Release date: | 2009-10-20 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.66 Å) | Cite: | Crystal structure of family 14 polysaccharide lyase with pH-dependent modes of action J.Biol.Chem., 284, 2009
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5H71
| Structure of alginate-binding protein AlgQ2 in complex with an alginate trisaccharide | Descriptor: | 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid, AlgQ2, CALCIUM ION, ... | Authors: | Uenishi, K, Kaneko, A, Maruyama, Y, Mikami, B, Murata, K, Hashimoto, W. | Deposit date: | 2016-11-15 | Release date: | 2017-08-09 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.549 Å) | Cite: | A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate J. Biol. Chem., 292, 2017
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1J1N
| Structure Analysis of AlgQ2, A Macromolecule(Alginate)-Binding Periplasmic Protein Of Sphingomonas Sp. A1., Complexed with an Alginate Tetrasaccharide | Descriptor: | AlgQ2, CALCIUM ION, beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid | Authors: | Momma, K, Mikami, B, Mishima, Y, Hashimoto, W, Murata, K. | Deposit date: | 2002-12-11 | Release date: | 2003-06-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1, complexed with an alginate tetrasaccharide at 1.6-A resolution J.BIOL.CHEM., 278, 2003
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1KWH
| Structure Analysis AlgQ2, a Macromolecule(alginate)-Binding Periplasmic Protein of Sphingomonas sp. A1. | Descriptor: | CALCIUM ION, Macromolecule-Binding Periplasmic Protein | Authors: | Momma, K, Mikami, B, Mishima, Y, Hashimoto, W, Murata, K. | Deposit date: | 2002-01-29 | Release date: | 2002-02-13 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1 at 2.0A resolution. J.Mol.Biol., 316, 2002
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1QXH
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6LRY
| Crystal structure of human endothelin ETB receptor in complex with sarafotoxin S6b | Descriptor: | Endothelin receptor type B,Endolysin,Endothelin receptor type B, Sarafotoxin-B | Authors: | Izume, T, Miyauchi, H, Shihoya, W, Nureki, O. | Deposit date: | 2020-01-16 | Release date: | 2020-02-12 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Crystal structure of human endothelin ETBreceptor in complex with sarafotoxin S6b. Biochem.Biophys.Res.Commun., 528, 2020
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2RGK
| Functional annotation of Escherichia coli yihS-encoded protein | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Uncharacterized sugar isomerase yihS | Authors: | Itoh, T, Mikami, B, Hashimoto, W, Murata, K. | Deposit date: | 2007-10-03 | Release date: | 2008-08-26 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Crystal structure of YihS in complex with D-mannose: structural annotation of Escherichia coli and Salmonella enterica yihS-encoded proteins to an aldose-ketose isomerase J.Mol.Biol., 377, 2008
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5GUB
| Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin disaccharide | Descriptor: | 1,2-ETHANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose, ... | Authors: | Oiki, S, Mikami, B, Murata, K, Hashimoto, W. | Deposit date: | 2016-08-26 | Release date: | 2017-07-19 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | A bacterial ABC transporter enables import of mammalian host glycosaminoglycans Sci Rep, 7, 2017
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3K8W
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8I2Z
| Cryo-EM structure of the zeaxanthin-bound kin4B8 | Descriptor: | RETINAL, Xanthorhodopsin, Zeaxanthin | Authors: | Murakoshi, S, Chazan, A, Shihoya, W, Beja, O, Nureki, O. | Deposit date: | 2023-01-15 | Release date: | 2023-03-29 | Last modified: | 2023-04-19 | Method: | ELECTRON MICROSCOPY (2 Å) | Cite: | Phototrophy by antenna-containing rhodopsin pumps in aquatic environments. Nature, 615, 2023
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5GX8
| Crystal structure of solute-binding protein related to glycosaminoglycans | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, D(-)-TARTARIC ACID, ... | Authors: | Oiki, S, Mikami, B, Murata, K, Hashimoto, W. | Deposit date: | 2016-09-15 | Release date: | 2017-07-19 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.778 Å) | Cite: | A bacterial ABC transporter enables import of mammalian host glycosaminoglycans Sci Rep, 7, 2017
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5GX6
| Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-4 position of GalNAc | Descriptor: | 1,2-ETHANEDIOL, 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose, CALCIUM ION, ... | Authors: | Oiki, S, Mikami, B, Murata, K, Hashimoto, W. | Deposit date: | 2016-09-15 | Release date: | 2017-07-26 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.81 Å) | Cite: | A bacterial ABC transporter enables import of mammalian host glycosaminoglycans Sci Rep, 7, 2017
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3K3T
| E185A mutant of peptidoglycan hydrolase from Sphingomonas sp. A1 | Descriptor: | Peptidoglycan hydrolase FlgJ, SULFATE ION | Authors: | Maruyama, Y, Ochiai, A, Itoh, T, Mikami, B, Hashimoto, W, Murata, K. | Deposit date: | 2009-10-04 | Release date: | 2010-07-14 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Mutational studies of the peptidoglycan hydrolase FlgJ of Sphingomonas sp. strain A1 J.Basic Microbiol., 50, 2010
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3K8V
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5GX7
| Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-6 position of GalNAc | Descriptor: | 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose, CALCIUM ION, Extracellular solute-binding protein family 1 | Authors: | Oiki, S, Mikami, B, Murata, K, Hashimoto, W. | Deposit date: | 2016-09-15 | Release date: | 2017-07-19 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.991 Å) | Cite: | A bacterial ABC transporter enables import of mammalian host glycosaminoglycans Sci Rep, 7, 2017
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6A6U
| Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation, in complex with FSA | Descriptor: | (4S,5S)-1,2-DITHIANE-4,5-DIOL, 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose, FLAVIN-ADENINE DINUCLEOTIDE, ... | Authors: | Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K. | Deposit date: | 2018-06-29 | Release date: | 2019-05-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.945 Å) | Cite: | Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Sci Rep, 9, 2019
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6A6T
| Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation | Descriptor: | (4S,5S)-1,2-DITHIANE-4,5-DIOL, FLAVIN-ADENINE DINUCLEOTIDE, Fructosyl amine: oxygen oxidoreductase, ... | Authors: | Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K. | Deposit date: | 2018-06-29 | Release date: | 2019-05-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.901 Å) | Cite: | Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Sci Rep, 9, 2019
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6A6V
| Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with 7 additional mutations, in complex with FSA | Descriptor: | 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose, FLAVIN-ADENINE DINUCLEOTIDE, Fructosyl amine: oxygen oxidoreductase | Authors: | Ogawa, N, Maruyama, Y, Itoh, T, Hashimoto, W, Murata, K. | Deposit date: | 2018-06-29 | Release date: | 2019-05-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Sci Rep, 9, 2019
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