2CXF
 
 | | RUN domain of Rap2 interacting protein x, crystallized in C2 space group | | Descriptor: | rap2 interacting protein x | | Authors: | Kukimoto-Niino, M, Murayama, K, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-06-29 | | Release date: | 2005-12-29 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (3.07 Å) | | Cite: | Crystal Structure of the RUN Domain of the RAP2-interacting Protein x
J.Biol.Chem., 281, 2006
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2EG9
 | | Crystal structure of the truncated extracellular domain of mouse CD38 | | Descriptor: | ADP-ribosyl cyclase 1 | | Authors: | Kukimoto-Niino, M, Mishima, C, Wakiyama, M, Terada, T, Shirouzu, M, Hara-Yokoyama, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-02-28 | | Release date: | 2008-03-11 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of the truncated extracellular domain of mouse CD38
To be Published
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2CXX
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2DBY
 | | Crystal structure of the GTP-binding protein YchF in complexed with GDP | | Descriptor: | FORMIC ACID, GTP-binding protein, GUANOSINE-5'-DIPHOSPHATE | | Authors: | Kukimoto-Niino, M, Murayama, K, Shirouzu, M, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-12-16 | | Release date: | 2006-06-16 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.76 Å) | | Cite: | Crystal structure of the GTP-binding protein YchF in complexed with GDP
To be Published
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2E0A
 | | Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with AMPPNP | | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, Pyruvate dehydrogenase kinase isozyme 4 | | Authors: | Kukimoto-Niino, M, Tokmakov, A, Terada, T, Shiromizu, I, Kawamoto, M, Matsusue, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-10-03 | | Release date: | 2007-10-09 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4.
Acta Crystallogr.,Sect.D, 67, 2011
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2EF1
 | | Crystal structure of the extracellular domain of human CD38 | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ADP-ribosyl cyclase 1 | | Authors: | Kukimoto-Niino, M, Nureki, O, Murayama, K, Shirouzu, M, Katada, T, Hara-Yokoyama, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-02-20 | | Release date: | 2007-02-27 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of the extracellular domain of human CD38
To be Published
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1X3S
 | | Crystal structure of human Rab18 in complex with Gppnhp | | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, Ras-related protein Rab-18 | | Authors: | Kukimoto-Niino, M, Murayama, K, Chen, L, Liu, Z.J, Wang, B.C, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-05-10 | | Release date: | 2005-11-10 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.32 Å) | | Cite: | Crystal structure of human Rab18 in complex with Gppnhp
To be Published
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2E87
 | | Crystal structure of hypothetical GTP-binding protein PH1320 from Pyrococcus horikoshii OT3, in complex with GDP | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Hypothetical protein PH1320, SULFATE ION | | Authors: | Kukimoto-Niino, M, Bessho, Y, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-01-19 | | Release date: | 2007-07-24 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Crystal structure of hypothetical GTP-binding protein PH1320 from Pyrococcus horikoshii OT3, in complex with GDP
To be Published
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2DYL
 | | Crystal structure of human mitogen-activated protein kinase kinase 7 activated mutant (S287D, T291D) | | Descriptor: | Dual specificity mitogen-activated protein kinase kinase 7 | | Authors: | Kukimoto-Niino, M, Takagi, T, Kaminishi, T, Uchikubo-Kamo, T, Terada, T, Matsuzaki, O, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-09-15 | | Release date: | 2007-08-28 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Crystal structure of human mitogen-activated protein kinase kinase 7 activated mutant (S287D, T291D)
To be Published
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2ZET
 | | Crystal structure of the small GTPase Rab27B complexed with the Slp homology domain of Slac2-a/melanophilin | | Descriptor: | GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, Melanophilin, ... | | Authors: | Kukimoto-Niino, M, Sakamoto, A, Kanno, E, Hanawa-Suetsugu, K, Terada, T, Shirouzu, M, Fukuda, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-12-17 | | Release date: | 2008-09-30 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structural basis for the exclusive specificity of Slac2-a/melanophilin for the Rab27 GTPases.
Structure, 16, 2008
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3AB3
 | | Crystal structure of p115RhoGEF RGS domain in complex with G alpha 13 | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Guanine nucleotide-binding protein G(k) subunit alpha, Guanine nucleotide-binding protein subunit alpha-13, ... | | Authors: | Kukimoto-Niino, M, Mishima, C, Shirouzu, M, Kozasa, T, Yokoyama, S. | | Deposit date: | 2009-11-30 | | Release date: | 2010-12-29 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Identification of critical residues in G(alpha)13 for stimulation of p115RhoGEF activity and the structure of the G(alpha)13-p115RhoGEF regulator of G protein signaling homology (RH) domain complex.
J.Biol.Chem., 286, 2011
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5AX9
 | | Crystal structure of the kinase domain of human TRAF2 and NCK-interacting protein kinase in complex with compund 9 | | Descriptor: | 4-methoxy-3-[2-[(3-methoxy-4-morpholin-4-yl-phenyl)amino]pyridin-4-yl]benzenecarbonitrile, SULFATE ION, TRAF2 and NCK-interacting protein kinase | | Authors: | Ohbayashi, N, Kukimoto-Niino, M, Yamada, T, Shirouzu, M. | | Deposit date: | 2015-07-21 | | Release date: | 2016-07-27 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | TNIK inhibition abrogates colorectal cancer stemness
Nat Commun, 7, 2016
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6JPP
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7Y4A
 | | Crystal structure of human ELMO1 RBD-RhoG complex | | Descriptor: | Engulfment and cell motility protein 1, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Tsuda, K, Kukimoto-Niino, M, Shirouzu, M. | | Deposit date: | 2022-06-14 | | Release date: | 2023-03-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Targeting Ras-binding domain of ELMO1 by computational nanobody design.
Commun Biol, 6, 2023
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5D7A
 | | Crystal structure of the kinase domain of TRAF2 and NCK-interacting protein kinase with NCB-0846 | | Descriptor: | SULFATE ION, TRAF2 and NCK-interacting protein kinase, cis-4-{[2-(1H-benzimidazol-5-ylamino)quinazolin-8-yl]oxy}cyclohexanol | | Authors: | Ohbayashi, N, Kukimoto-Niino, M, Yamada, T, Shirouzu, M. | | Deposit date: | 2015-08-13 | | Release date: | 2016-08-17 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | TNIK inhibition abrogates colorectal cancer stemness
Nat Commun, 7, 2016
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5CWZ
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7XN1
 | | Crystal structure of human acetylcholinesterase in complex with tacrine | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL, Acetylcholinesterase, ... | | Authors: | Dileep, K.V, Ihara, K, Mishima-Tsumagari, C, Kukimoto-Niino, M, Yonemochi, M, Hanada, K, Shirouzu, M, Zhang, K.Y.J. | | Deposit date: | 2022-04-27 | | Release date: | 2023-03-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Crystal structure of human acetylcholinesterase in complex with tacrine: Implications for drug discovery
Int.J.Biol.Macromol., 210, 2022
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2PSM
 | | Crystal structure of Interleukin 15 in complex with Interleukin 15 receptor alpha | | Descriptor: | BENZAMIDINE, Interleukin-15, Interleukin-15 receptor alpha chain | | Authors: | Olsen, S.K, Murayama, K, Kishishita, S, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Ota, N, Kanagawa, O, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-05-07 | | Release date: | 2007-11-06 | | Last modified: | 2021-08-18 | | Method: | X-RAY DIFFRACTION (2.19 Å) | | Cite: | Crystal Structure of the Interleukin-15{middle dot}Interleukin-15 Receptor {alpha} Complex: INSIGHTS INTO TRANS AND CIS PRESENTATION
J.Biol.Chem., 282, 2007
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7E3D
 | | Crystal structure of human acetylcholinesterase | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL, Acetylcholinesterase | | Authors: | Dileep, K.V, Ihara, K, Mishima-Tsumagari, C, Kukimoto-Niino, M, Yonemochi, M, Hanada, K, Shirouzu, M, Zhang, K.Y.J. | | Deposit date: | 2021-02-08 | | Release date: | 2022-02-16 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of human acetylcholinesterase in complex with tacrine: Implications for drug discovery
Int.J.Biol.Macromol., 210, 2022
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7E3H
 | | Crystal structure of human acetylcholinesterase in complex with donepezil | | Descriptor: | 1-BENZYL-4-[(5,6-DIMETHOXY-1-INDANON-2-YL)METHYL]PIPERIDINE, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Acetylcholinesterase | | Authors: | Dileep, K.V, Ihara, K, Mishima-Tsumagari, C, Kukimoto-Niino, M, Yonemochi, M, Hanada, K, Shirouzu, M, Zhang, K.Y.J. | | Deposit date: | 2021-02-08 | | Release date: | 2022-02-16 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Crystal structure of human acetylcholinesterase in complex with tacrine: Implications for drug discovery
Int.J.Biol.Macromol., 210, 2022
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3AQE
 | | Crystal structure of the extracellular domain of human RAMP2 | | Descriptor: | Receptor activity-modifying protein 2 | | Authors: | Kusano, S, Kukimoto-Niino, M, Shirouzu, M, Shindo, T, Yokoyama, S. | | Deposit date: | 2010-10-29 | | Release date: | 2011-11-09 | | Last modified: | 2012-07-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis for extracellular interactions between calcitonin receptor-like receptor and receptor activity-modifying protein 2 for adrenomedullin-specific binding
Protein Sci., 21, 2012
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3B13
 | | Crystal structure of the DHR-2 domain of DOCK2 in complex with Rac1 (T17N mutant) | | Descriptor: | Dedicator of cytokinesis protein 2, Ras-related C3 botulinum toxin substrate 1 | | Authors: | Hanawa-Suetsugu, K, Kukimoto-Niino, M, Mishima-Tsumagari, C, Terada, T, Shirouzu, M, Fukui, Y, Yokoyama, S. | | Deposit date: | 2011-06-24 | | Release date: | 2012-03-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3.006 Å) | | Cite: | Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.
Proc.Natl.Acad.Sci.USA, 109, 2012
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5ZJ6
 | | Crystal structure of HCK kinase complexed with a pyrrolo-pyrimidine inhibitor 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine | | Descriptor: | 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine, Tyrosine-protein kinase HCK | | Authors: | Tomabechi, Y, Kukimoto-Niino, M, Shirouzu, M. | | Deposit date: | 2018-03-19 | | Release date: | 2018-06-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.696 Å) | | Cite: | Phosphorylated and non-phosphorylated HCK kinase domains produced by cell-free protein expression.
Protein Expr. Purif., 150, 2018
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5GV3
 | | Crystal structure of the membrane-distal domain of mouse lysosome-associated membrane protein 2 (LAMP-2) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Lysosome-associated membrane glycoprotein 2, ZINC ION | | Authors: | Tomabechi, Y, Ehara, H, Kukimoto-Niino, M, Shirouzu, M. | | Deposit date: | 2016-09-01 | | Release date: | 2017-09-06 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.096 Å) | | Cite: | Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes.
Biochem. Biophys. Res. Commun., 479, 2016
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5GV0
 | | Crystal structure of the membrane-proximal domain of mouse lysosome-associated membrane protein 1 (LAMP-1) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Lysosome-associated membrane glycoprotein 1, SULFATE ION | | Authors: | Tomabechi, Y, Ehara, H, Kukimoto-Niino, M, Shirouzu, M. | | Deposit date: | 2016-09-01 | | Release date: | 2016-10-12 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes
Biochem.Biophys.Res.Commun., 479, 2016
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