5GQI
| Crystal structure of Cypovirus Polyhedra mutant with deletion of Ala194 | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ... | Authors: | Abe, S, Tabe, H, Ijiri, H, Yamashita, K, Hirata, K, Mori, H, Ueno, T. | Deposit date: | 2016-08-07 | Release date: | 2017-02-15 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.3 Å) | Cite: | Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells ACS Nano, 11, 2017
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5GQL
| Crystal structure of Wild Type Cypovirus Polyhedra | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ... | Authors: | Abe, S, Tabe, H, Ijiri, H, Yamashita, K, Hirata, K, Mori, H, Ueno, T. | Deposit date: | 2016-08-07 | Release date: | 2017-02-15 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells ACS Nano, 11, 2017
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5GQJ
| Crystal structure of Cypovirus Polyhedra mutant with deletion of Ser193 and Ala194 | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ... | Authors: | Abe, S, Tabe, H, Ijiri, H, Yamashita, K, Hirata, K, Mori, H, Ueno, T. | Deposit date: | 2016-08-07 | Release date: | 2017-02-15 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells ACS Nano, 11, 2017
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5GQM
| Crystal structure of in cellulo Wild Type Cypovirus Polyhedra | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, CYTIDINE-5'-TRIPHOSPHATE, ... | Authors: | Abe, S, Tabe, H, Ijiri, H, Yamashita, K, Hirata, K, Mori, H, Ueno, T. | Deposit date: | 2016-08-07 | Release date: | 2017-02-15 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.68 Å) | Cite: | Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells ACS Nano, 11, 2017
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2EIL
| Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized state | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | Authors: | Muramoto, K, Hirata, K, Shinzawa-Itoh, K, Yoko-o, S, Yamashita, E, Aoyama, H, Tsukihara, T, Yoshikawa, S. | Deposit date: | 2007-03-13 | Release date: | 2007-05-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase Proc.Natl.Acad.Sci.Usa, 104, 2007
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2EIN
| Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized state | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | Authors: | Muramoto, K, Hirata, K, Shinzawa-Itoh, K, Yoko-o, S, Yamashita, E, Aoyama, H, Tsukihara, T, Yoshikawa, S. | Deposit date: | 2007-03-13 | Release date: | 2007-05-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase Proc.Natl.Acad.Sci.Usa, 104, 2007
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2EIK
| Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | Authors: | Muramoto, K, Hirata, K, Shinzawa-Itoh, K, Yoko-O, S, Yamashita, E, Aoyama, H, Tsukihara, T, Yoshikawa, S. | Deposit date: | 2007-03-13 | Release date: | 2007-05-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase Proc.Natl.Acad.Sci.Usa, 104, 2007
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2EIJ
| Bovine heart cytochrome C oxidase in the fully reduced state | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | Authors: | Muramoto, K, Hirata, K, Shinzawa-Itoh, K, Yoko-o, S, Yamashita, E, Aoyama, H, Tsukihara, T, Yoshikawa, S. | Deposit date: | 2007-03-13 | Release date: | 2007-05-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase Proc.Natl.Acad.Sci.Usa, 104, 2007
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2EIM
| Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | Authors: | Muramoto, K, Hirata, K, Shinzawa-Itoh, K, Yoko-o, S, Yamashita, E, Aoyama, H, Tsukihara, T, Yoshikawa, S. | Deposit date: | 2007-03-13 | Release date: | 2007-05-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase Proc.Natl.Acad.Sci.Usa, 104, 2007
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7DVO
| Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ... | Authors: | Nomura, T, Kimura, T, Kanematsu, Y, Yamashita, K, Hirata, K, Ueno, G, Murakami, H, Hisano, T, Yamagiwa, R, Takeda, H, Gopalasingam, C, Yuki, K, Kousaka, R, Yanagasawa, S, Shoji, O, Kumasaka, T, Takano, Y, Ago, H, Yamamoto, M, Sugimoto, H, Tosha, T, Kubo, M, Shiro, Y. | Deposit date: | 2021-01-14 | Release date: | 2021-05-19 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Short-lived intermediate in N 2 O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography. Proc.Natl.Acad.Sci.USA, 118, 2021
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6L63
| Human Coagulation Factor XIIa (FXIIa) bound with the macrocyclic peptide F3 containing two (1S,2S)-2-ACHC residues | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ACETYL GROUP, ... | Authors: | Sengoku, T, Katoh, T, Hirata, K, Suga, H, Ogata, K. | Deposit date: | 2019-10-26 | Release date: | 2020-09-02 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Ribosomal synthesis and de novo discovery of bioactive foldamer peptides containing cyclic beta-amino acids. Nat.Chem., 12, 2020
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6LEE
| Crystal structure of Cypovirus Polyhedra mutant with deletion of Ala67-Ala104 | Descriptor: | Polyhedrin | Authors: | Abe, S, Kasamatsu, M, Hirata, K, Yamashita, K, Ueno, T. | Deposit date: | 2019-11-25 | Release date: | 2020-12-09 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | In-Cell Engineering of Protein Crystals with Nanoporous Structures for Promoting Cascade Reactions ACS Appl Nano Mater, 4, 2021
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6KS2
| Structure of anti-Ghrelin receptor antibody | Descriptor: | Fab7881 Heavy Chain (FabH), Fab7881 Light Chain (FabL) | Authors: | Shiimura, Y, Horita, S, Asada, H, Hirata, K, Iwata, S, Kojima, M. | Deposit date: | 2019-08-23 | Release date: | 2020-08-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.753 Å) | Cite: | Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode. Nat Commun, 11, 2020
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6KO5
| Complex structure of Ghrelin receptor with Fab | Descriptor: | 6-(4-bromanyl-2-fluoranyl-phenoxy)-2-methyl-3-[[(3~{S})-1-propan-2-ylpiperidin-3-yl]methyl]pyrido[3,2-d]pyrimidin-4-one, Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1, Fab7881 Heavy Chain, ... | Authors: | Shiimura, Y, Horita, S, Asada, H, Hirata, K, Iwata, S, Kojima, M. | Deposit date: | 2019-08-08 | Release date: | 2020-08-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode. Nat Commun, 11, 2020
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7E3E
| Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Cysteine peptidase C (CPC), beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Abe, S, Pham, T.T, Negishi, H, Yamashita, K, Hirata, K, Ueno, T. | Deposit date: | 2021-02-08 | Release date: | 2021-12-15 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Design of an In-Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament. Angew.Chem.Int.Ed.Engl., 60, 2021
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7E3G
| Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant in the living cell | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Cysteine peptidase C (CPC), beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Abe, S, Pham, T.T, Negishi, H, Yamashita, K, Hirata, K, Ueno, T. | Deposit date: | 2021-02-08 | Release date: | 2021-12-15 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.86 Å) | Cite: | Design of an In-Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament. Angew.Chem.Int.Ed.Engl., 60, 2021
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7E3F
| Crystal structure of Trypanosoma brucei cathepsin B Y217C/S275C mutant | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Cysteine peptidase C (CPC), beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Abe, S, Pham, T.T, Negishi, H, Yamashita, K, Hirata, K, Ueno, T. | Deposit date: | 2021-02-08 | Release date: | 2021-12-15 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Design of an In-Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament. Angew.Chem.Int.Ed.Engl., 60, 2021
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7BU7
| Structure of human beta1 adrenergic receptor bound to BI-167107 and nanobody 6B9 | Descriptor: | (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one, ... | Authors: | Xu, X, Kaindl, J, Clark, M, Hubner, H, Hirata, K, Sunahara, R, Gmeiner, P, Kobilka, B.K, Liu, X. | Deposit date: | 2020-04-04 | Release date: | 2020-12-02 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Binding pathway determines norepinephrine selectivity for the human beta 1 AR over beta 2 AR. Cell Res., 31, 2021
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7BVQ
| Structure of human beta1 adrenergic receptor bound to carazolol | Descriptor: | (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol, (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate, CHOLESTEROL, ... | Authors: | Xu, X, Kaindl, J, Clark, M, Hubner, H, Hirata, K, Sunahara, R, Gmeiner, P, Kobilka, B.K, Liu, X. | Deposit date: | 2020-04-11 | Release date: | 2020-12-02 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Binding pathway determines norepinephrine selectivity for the human beta 1 AR over beta 2 AR. Cell Res., 31, 2021
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7BU6
| Structure of human beta1 adrenergic receptor bound to norepinephrine and nanobody 6B9 | Descriptor: | (2S)-2,3-dihydroxypropyl octanoate, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CHOLESTEROL, ... | Authors: | Xu, X, Kaindl, J, Clark, M, Hubner, H, Hirata, K, Sunahara, R, Gmeiner, P, Kobilka, B.K, Liu, X. | Deposit date: | 2020-04-04 | Release date: | 2020-12-02 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Binding pathway determines norepinephrine selectivity for the human beta 1 AR over beta 2 AR. Cell Res., 31, 2021
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7BTS
| Structure of human beta1 adrenergic receptor bound to epinephrine and nanobody 6B9 | Descriptor: | (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CHOLESTEROL, ... | Authors: | Xu, X, Kaindl, J, Clark, M, Hubner, H, Hirata, K, Sunahara, R, Gmeiner, P, Kobilka, B.K, Liu, X. | Deposit date: | 2020-04-02 | Release date: | 2020-12-02 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.13 Å) | Cite: | Binding pathway determines norepinephrine selectivity for the human beta 1 AR over beta 2 AR. Cell Res., 31, 2021
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2ZXW
| Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset) | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | Authors: | Aoyama, H, Muramoto, K, Shinzawa-Itoh, K, Hirata, K, Yamashita, E, Tsukihara, T, Ogura, T, Yoshikawa, S. | Deposit date: | 2009-01-08 | Release date: | 2009-02-24 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump Proc.Natl.Acad.Sci.USA, 106, 2009
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7C4S
| Sphingosine-1-phosphate receptor 3 with a natural ligand. | Descriptor: | (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate, Antibody Fab fragment heavy chain, Antibody Fab fragment light chain, ... | Authors: | Iwata, S, Maeda, S, Luo, F, Nango, E, hirata, K, Asada, H. | Deposit date: | 2020-05-18 | Release date: | 2021-06-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Endogenous agonist-bound S1PR3 structure reveals determinants of G protein-subtype bias. Sci Adv, 7, 2021
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7VG7
| Plexin B1 extracellular fragment in complex with lasso-grafted PB1m6A9 peptide | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Plexin-B1, TRIETHYLENE GLYCOL, ... | Authors: | Sugano, N.N, Hirata, K, Yamashita, K, Yamamoto, M, Arimori, T, Takagi, J. | Deposit date: | 2021-09-14 | Release date: | 2022-08-17 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | De novo Fc-based receptor dimerizers differentially modulate PlexinB1 function. Structure, 30, 2022
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7VF3
| Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, DI(HYDROXYETHYL)ETHER, Plexin-B1, ... | Authors: | Sugano, N.N, Hirata, K, Yamashita, K, Yamamoto, M, Arimori, T, Takagi, J. | Deposit date: | 2021-09-10 | Release date: | 2022-08-17 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.29 Å) | Cite: | De novo Fc-based receptor dimerizers differentially modulate PlexinB1 function. Structure, 30, 2022
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