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1GAX
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BU of 1gax by Molmil
CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE
Descriptor: N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE, TRNA(VAL), VALYL-TRNA SYNTHETASE, ...
Authors:Fukai, S, Nureki, O, Sekine, S, Shimada, A, Tao, J, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2000-06-23
Release date:2000-12-06
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase.
Cell(Cambridge,Mass.), 103, 2000
1IVS
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BU of 1ivs by Molmil
CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE
Descriptor: N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE, Valyl-tRNA synthetase, tRNA (Val)
Authors:Fukai, S, Nureki, O, Sekine, S.-I, Shimada, A, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2002-03-29
Release date:2003-02-11
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
RNA, 9, 2003
1IYW
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BU of 1iyw by Molmil
Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase
Descriptor: Valyl-tRNA Synthetase
Authors:Fukai, S, Nureki, O, Sekine, S, Shimada, A, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2002-09-10
Release date:2003-06-17
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (4 Å)
Cite:Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
RNA, 9, 2003
1UAD
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BU of 1uad by Molmil
Crystal structure of the RalA-GppNHp-Sec5 Ral-binding domain complex
Descriptor: Exocyst complex component Sec5, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, ...
Authors:Fukai, S, Matern, H.T, Scheller, R.H, Brunger, A.T.
Deposit date:2003-03-09
Release date:2003-07-15
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structural basis of the interaction between RalA and Sec5, a subunit of the Sec6/8 complex
EMBO J., 22, 2003
2E7S
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BU of 2e7s by Molmil
Crystal structure of the yeast Sec2p GEF domain
Descriptor: Rab guanine nucleotide exchange factor SEC2
Authors:Fukai, S, Sato, Y, Nureki, O.
Deposit date:2007-01-12
Release date:2007-02-27
Last modified:2021-11-10
Method:X-RAY DIFFRACTION (3 Å)
Cite:Asymmetric Coiled-Coil Structure with Guanine Nucleotide Exchange Activity
Structure, 15, 2007
4WU5
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BU of 4wu5 by Molmil
HLA-A24 in complex with HIV-1 Nef134-8(wt)
Descriptor: 8-Mer peptide from Protein Nef, Beta-2-microglobulin, HLA class I histocompatibility antigen, ...
Authors:Shimizu, A, Yamagata, A, Fukai, S, Iwamoto, A.
Deposit date:2014-10-31
Release date:2015-05-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure of Nef134-8(wt) epitope presented by HLA-A24
To Be Published
4UBQ
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BU of 4ubq by Molmil
Crystal Structure of IMP-2 Metallo-beta-Lactamase from Acinetobacter spp.
Descriptor: ACETATE ION, Beta-lactamase, ZINC ION
Authors:Yamaguchi, Y, Matsueda, S, Matsunaga, K, Takashio, N, Toma-Fukai, S, Yamagata, Y, Shibata, N, Wachino, J, Shibayama, K, Arakawa, Y, Kurosaki, H.
Deposit date:2014-08-13
Release date:2014-12-24
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structure of IMP-2 metallo-beta-lactamase from Acinetobacter spp.: comparison of active-site loop structures between IMP-1 and IMP-2.
Biol.Pharm.Bull., 38, 2015
8J6N
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BU of 8j6n by Molmil
Crystal structure of Cystathionine gamma-lyase in complex with compound 1
Descriptor: 1,2-ETHANEDIOL, Cystathionine gamma-lyase, GLYCEROL, ...
Authors:Hibi, R, Toma-Fukai, S, Shimizu, T, Hanaoka, K.
Deposit date:2023-04-26
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Discovery of a cystathionine gamma-lyase (CSE) selective inhibitor targeting active-site pyridoxal 5'-phosphate (PLP) via Schiff base formation.
Sci Rep, 13, 2023
7BY1
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BU of 7by1 by Molmil
Crystal structure of GCN5 PCAF N-terminal domain
Descriptor: Histone acetyltransferase KAT2A, ZINC ION
Authors:Hibi, R, Toma-Fukai, S, Shimizu, T.
Deposit date:2020-04-21
Release date:2020-08-26
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure.
J.Biol.Chem., 295, 2020
7CQF
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BU of 7cqf by Molmil
Crystal structure of PSD-95 PDZ3 fused with ADAM22 C-terminal peptide
Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, CHOLINE ION, ...
Authors:Yamagata, A, Fukai, S.
Deposit date:2020-08-10
Release date:2021-01-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:LGI1-ADAM22-MAGUK configures transsynaptic nanoalignment for synaptic transmission and epilepsy prevention.
Proc.Natl.Acad.Sci.USA, 118, 2021
5B86
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BU of 5b86 by Molmil
Crystal structure of M-Sec
Descriptor: Tumor necrosis factor alpha-induced protein 2
Authors:Yamashita, M, Sato, Y, Yamagata, A, Fukai, S.
Deposit date:2016-06-12
Release date:2016-10-12
Last modified:2020-02-26
Method:X-RAY DIFFRACTION (3.017 Å)
Cite:Distinct Roles for the N- and C-terminal Regions of M-Sec in Plasma Membrane Deformation during Tunneling Nanotube Formation.
Sci Rep, 6, 2016
5DST
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BU of 5dst by Molmil
Crystal structure of human PRMT8 in complex with SAH
Descriptor: Protein arginine N-methyltransferase 8, S-ADENOSYL-L-HOMOCYSTEINE
Authors:Toma-Fukai, S, Shimizu, T.
Deposit date:2015-09-17
Release date:2016-02-24
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.963 Å)
Cite:Novel helical assembly in arginine methyltransferase 8
J.Mol.Biol., 428, 2016
5GVC
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BU of 5gvc by Molmil
Human Topoisomerase IIIb topo domain
Descriptor: DNA topoisomerase 3-beta-1, MAGNESIUM ION
Authors:Goto-Ito, S, Yamagata, A, Sato, Y, Takahashi, T.S, Fukai, S.
Deposit date:2016-09-05
Release date:2017-06-14
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.436 Å)
Cite:Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Sci Rep, 7, 2017
5GVD
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BU of 5gvd by Molmil
Human TDRD3 DUF1767-OB domains
Descriptor: 1,2-ETHANEDIOL, MAGNESIUM ION, PHOSPHATE ION, ...
Authors:Goto-Ito, S, Yamagata, A, Sato, Y, Takahashi, T.S, Fukai, S.
Deposit date:2016-09-05
Release date:2017-06-14
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.623 Å)
Cite:Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Sci Rep, 7, 2017
5GVE
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BU of 5gve by Molmil
Human TOP3B-TDRD3 complex
Descriptor: DNA topoisomerase 3-beta-1, MAGNESIUM ION, Tudor domain-containing protein 3
Authors:Goto-Ito, S, Yamagata, A, Sato, Y, Takahashi, T.S, Fukai, S.
Deposit date:2016-09-05
Release date:2017-06-14
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.606 Å)
Cite:Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Sci Rep, 7, 2017
7CEE
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BU of 7cee by Molmil
Crystal structure of mouse neuroligin-3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Neuroligin-3
Authors:Yamagata, A, Yoshida, T, Shiroshima, T, Maeda, A, Fukai, S.
Deposit date:2020-06-23
Release date:2021-02-24
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.763 Å)
Cite:Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice.
Nat Commun, 12, 2021
7CEG
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BU of 7ceg by Molmil
Crystal structure of the complex between mouse PTP delta and neuroligin-3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Isoform C of Receptor-type tyrosine-protein phosphatase delta, Neuroligin-3
Authors:Yamagata, A, Yoshida, T, Shiroshima, T, Maeda, A, Fukai, S.
Deposit date:2020-06-23
Release date:2021-02-24
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.85 Å)
Cite:Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice.
Nat Commun, 12, 2021
5H11
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BU of 5h11 by Molmil
Crystal structure of Zebrafish Sec10
Descriptor: BROMIDE ION, Uncharacterized protein
Authors:Chen, J, Yamagata, A, Fukai, S.
Deposit date:2016-10-07
Release date:2017-02-01
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.732 Å)
Cite:Crystal structure of Sec10, a subunit of the exocyst complex
Sci Rep, 7, 2017
5GVI
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BU of 5gvi by Molmil
Zebrafish USP30 in complex with Lys6-linked diubiquitin
Descriptor: Ubiquitin carboxyl-terminal hydrolase 30, ZINC ION, ubiquitin
Authors:Sato, Y, Fukai, S.
Deposit date:2016-09-05
Release date:2017-09-13
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30
Nat. Struct. Mol. Biol., 24, 2017
4YH7
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BU of 4yh7 by Molmil
Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Interleukin-1 receptor accessory protein-like 1, ...
Authors:Yamagata, A, Fukai, S.
Deposit date:2015-02-27
Release date:2015-05-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (4.4 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
4YFE
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BU of 4yfe by Molmil
Crystal structure of PTP delta Fn1-Fn2
Descriptor: Receptor-type tyrosine-protein phosphatase delta
Authors:Yamagata, A, Fukai, S.
Deposit date:2015-02-25
Release date:2015-05-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.972 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
4YFG
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BU of 4yfg by Molmil
Crystal structure of PTP delta meA3/meB minus variant Ig1-Fn1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Receptor-type tyrosine-protein phosphatase delta
Authors:Yamagata, A, Fukai, S.
Deposit date:2015-02-25
Release date:2015-05-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.491 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
4YH6
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BU of 4yh6 by Molmil
Crystal structure of IL1RAPL1 ectodomain
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Interleukin-1 receptor accessory protein-like 1, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Yamagata, A, Fukai, S.
Deposit date:2015-02-27
Release date:2015-05-06
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (3 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
4YFD
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BU of 4yfd by Molmil
Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Interleukin-1 receptor accessory protein, Receptor-type tyrosine-protein phosphatase delta
Authors:Yamagata, A, Fukai, S.
Deposit date:2015-02-25
Release date:2015-05-06
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.253 Å)
Cite:Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
4Y61
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BU of 4y61 by Molmil
Crystal structure of the complex between Slitrk2 LRR1 and PTP delta Ig1-Fn1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Receptor-type tyrosine-protein phosphatase delta, SLIT and NTRK-like protein 2
Authors:Yamgata, A, Sato, Y, Goto-Ito, S, Uemura, T, Maeda, A, Shiroshima, T, Yoshida, T, Fukai, S.
Deposit date:2015-02-12
Release date:2015-06-03
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.358 Å)
Cite:Structure of Slitrk2-PTP delta complex reveals mechanisms for splicing-dependent trans-synaptic adhesion.
Sci Rep, 5, 2015

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