6KNB
 
 | | PolD-PCNA-DNA (form A) | | Descriptor: | DNA polymerase D DP2 (DNA polymerase II large) subunit, DNA polymerase II small subunit, DNA polymerase sliding clamp 1, ... | | Authors: | Mayanagi, K, Oki, K, Miyazaki, N, Ishino, S, Yamagami, T, Iwasaki, K, Kohda, D, Morikawa, K, Shirai, T, Ishino, Y. | | Deposit date: | 2019-08-05 | | Release date: | 2020-08-05 | | Last modified: | 2021-02-17 | | Method: | ELECTRON MICROSCOPY (6.9 Å) | | Cite: | Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
Bmc Biol., 18, 2020
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6KNC
 | | PolD-PCNA-DNA (form B) | | Descriptor: | DNA polymerase D DP2 (DNA polymerase II large) subunit, DNA polymerase II small subunit, DNA polymerase sliding clamp 1, ... | | Authors: | Mayanagi, K, Oki, K, Miyazaki, N, Ishino, S, Yamagami, T, Iwasaki, K, Kohda, D, Morikawa, K, Shirai, T, Ishino, Y. | | Deposit date: | 2019-08-05 | | Release date: | 2020-08-05 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (9.3 Å) | | Cite: | Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
Bmc Biol., 18, 2020
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1Z5R
 | | Crystal Structure of Activated Porcine Pancreatic Carboxypeptidase B | | Descriptor: | ZINC ION, procarboxypeptidase B | | Authors: | Adler, M, Bryant, J, Buckman, B, Islam, I, Larsen, B, Finster, S, Kent, L, May, K, Mohan, R, Yuan, S, Whitlow, M. | | Deposit date: | 2005-03-18 | | Release date: | 2005-07-12 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Crystal structures of potent thiol-based inhibitors bound to carboxypeptidase b.
Biochemistry, 44, 2005
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1ZG9
 | | Crystal Structure of 5-{[amino(imino)methyl]amino}-2-(sulfanylmethyl)pentanoic acid Bound to Activated Porcine Pancreatic Carboxypeptidase B | | Descriptor: | 5-{[AMINO(IMINO)METHYL]AMINO}-2-(SULFANYLMETHYL)PENTANOIC ACID, ZINC ION, procarboxypeptidase B | | Authors: | Adler, M, Bryant, J, Buckman, B, Islam, I, Larsen, B, Finster, S, Kent, L, May, K, Mohan, R, Yuan, S, Whitlow, M. | | Deposit date: | 2005-04-20 | | Release date: | 2005-07-12 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structures of potent thiol-based inhibitors bound to carboxypeptidase b.
Biochemistry, 44, 2005
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1ZG8
 | | Crystal Structure of (R)-2-(3-{[amino(imino)methyl]amino}phenyl)-3-sulfanylpropanoic acid Bound to Activated Porcine Pancreatic Carboxypeptidase B | | Descriptor: | (2R)-2-(3-{[AMINO(IMINO)METHYL]AMINO}PHENYL)-3-SULFANYLPROPANOIC ACID, ZINC ION, procarboxypeptidase B | | Authors: | Adler, M, Bryant, J, Buckman, B, Islam, I, Larsen, B, Finster, S, Kent, L, May, K, Mohan, R, Yuan, S, Whitlow, M. | | Deposit date: | 2005-04-20 | | Release date: | 2005-07-12 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structures of potent thiol-based inhibitors bound to carboxypeptidase b.
Biochemistry, 44, 2005
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1ZG7
 | | Crystal Structure of 2-(5-{[amino(imino)methyl]amino}-2-chlorophenyl)-3-sulfanylpropanoic acid Bound to Activated Porcine Pancreatic Carboxypeptidase B | | Descriptor: | 2-(5-{[AMINO(IMINO)METHYL]AMINO}-2-CHLOROPHENYL)-3-SULFANYLPROPANOIC ACID, ZINC ION, procarboxypeptidase B | | Authors: | Adler, M, Bryant, J, Buckman, B, Islam, I, Larsen, B, Finster, S, Kent, L, May, K, Mohan, R, Yuan, S, Whitlow, M. | | Deposit date: | 2005-04-20 | | Release date: | 2005-07-12 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Crystal structures of potent thiol-based inhibitors bound to carboxypeptidase b.
Biochemistry, 44, 2005
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5GKI
 | | Structure of EndoMS-dsDNA3 complex | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*GP*CP*CP*TP*AP*GP*GP*TP*CP*CP*CP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*GP*GP*GP*GP*CP*CP*TP*AP*GP*GP*C)-3'), ... | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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5GKG
 | | Structure of EndoMS-dsDNA1'' complex | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*GP*GP*TP*CP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3'), ... | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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5GKJ
 | | Structure of EndoMS in apo form | | Descriptor: | Endonuclease EndoMS | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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5GKF
 | | Structure of EndoMS-dsDNA1' complex | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*TP*TP*GP*TP*AP*GP*CP*G)-3'), ... | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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5GKE
 | | Structure of EndoMS-dsDNA1 complex | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3'), ... | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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5GKH
 | | Structure of EndoMS-dsDNA2 complex | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*AP*CP*GP*GP*CP*AP*CP*TP*TP*GP*GP*CP*AP*CP*G)-3'), DNA (5'-D(*CP*GP*TP*GP*CP*CP*AP*GP*GP*TP*GP*CP*CP*GP*T)-3'), ... | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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8YTE
 | | Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide | | Descriptor: | 1,2-ETHANEDIOL, AMINOMETHYLAMIDE, High affinity nerve growth factor receptor, ... | | Authors: | Yamada, T, Mihara, K, Ueda, T, Yamauchi, D, Shimizu, M, Ando, A, Mayumi, K, Nakata, Z, Mikamiyama, H. | | Deposit date: | 2024-03-25 | | Release date: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (2.26 Å) | | Cite: | Discovery and Hit to Lead Optimization of Macrocyclic Peptides as Novel Tropomyosin Receptor Kinase A Antagonists
J.Med.Chem., 2024
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8YTD
 | | Crystal Structure of TrkA D5 domain in complex with two different macrocyclic peptides | | Descriptor: | 1,2-ETHANEDIOL, High affinity nerve growth factor receptor, Macrocyclic Peptide | | Authors: | Yamada, T, Mihara, K, Ueda, T, Yamauchi, D, Shimizu, M, Ando, A, Mayumi, K, Nakata, Z, Mikamiyama, H. | | Deposit date: | 2024-03-25 | | Release date: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (2.34 Å) | | Cite: | Discovery and Hit to Lead Optimization of Macrocyclic Peptides as Novel Tropomyosin Receptor Kinase A Antagonists
J.Med.Chem., 2024
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4HTM
 | | Mechanism of CREB Recognition and Coactivation by the CREB Regulated Transcriptional Coactivator CRTC2 | | Descriptor: | CREB-regulated transcription coactivator 2, ZINC ION | | Authors: | Luo, Q, Viste, K, Urday-Zaa, J.C, Kumar, G.S, Tsai, W.-W, Talai, A, Mayo, K, Montminy, M, Radhakrishnan, I. | | Deposit date: | 2012-11-01 | | Release date: | 2012-12-05 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Protein kinase N1, a cell inhibitor of Akt kinase, has a central role in quality control of germinal center formation
Proc.Natl.Acad.Sci.USA, 2012
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1HQC
 | | STRUCTURE OF RUVB FROM THERMUS THERMOPHILUS HB8 | | Descriptor: | ADENINE, MAGNESIUM ION, RUVB | | Authors: | Yamada, K, Kunishima, N, Mayanagi, K, Iwasaki, H, Morikawa, K. | | Deposit date: | 2000-12-15 | | Release date: | 2001-02-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8.
Proc.Natl.Acad.Sci.USA, 98, 2001
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1IXS
 | | Structure of RuvB complexed with RuvA domain III | | Descriptor: | Holliday junction DNA helicase ruvA, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, RuvB | | Authors: | Yamada, K, Miyata, T, Tsuchiya, D, Oyama, T, Fujiwara, Y, Ohnishi, T, Iwasaki, H, Shinagawa, H, Ariyoshi, M, Mayanagi, K, Morikawa, K. | | Deposit date: | 2002-07-04 | | Release date: | 2002-11-06 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Crystal Structure of the RuvA-RuvB Complex: A Structural Basis for the Holliday Junction Migrating Motor Machinery
Mol.Cell, 10, 2002
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1IXR
 | | RuvA-RuvB complex | | Descriptor: | Holliday junction DNA helicase ruvA, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, RuvB | | Authors: | Yamada, K, Miyata, T, Tsuchiya, D, Oyama, T, Fujiwara, Y, Ohnishi, T, Iwasaki, H, Shinagawa, H, Ariyoshi, M, Mayanagi, K, Morikawa, K. | | Deposit date: | 2002-07-04 | | Release date: | 2002-11-06 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Crystal Structure of the RuvA-RuvB Complex: A Structural Basis for the Holliday Junction Migrating Motor Machinery
Mol.Cell, 10, 2002
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3A57
 | | Crystal structure of Thermostable Direct Hemolysin | | Descriptor: | Thermostable direct hemolysin 2 | | Authors: | Hashimoto, H, Yanagihara, I, Nakahira, K, Hamada, D, Ikegami, T, Mayanagi, K, Kaieda, S, Fukui, T, Ohnishi, K, Kajiyama, S, Yamane, T, Ikeguchi, M, Honda, T, Shimizu, T, Sato, M. | | Deposit date: | 2009-08-03 | | Release date: | 2010-03-31 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin
J.Biol.Chem., 285, 2010
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4CST
 | | Crystal structure of FimH in complex with 3'-Chloro-4'-(alpha-D-mannopyranosyloxy)-biphenyl-4-carbonitrile | | Descriptor: | 3'-chloro-4'-(alpha-D-mannopyranosyloxy)biphenyl-4-carbonitrile, PROTEIN FIMH | | Authors: | Kleeb, S, Pang, L, Mayer, K, Sigl, A, Eris, D, Preston, R.C, Zihlmann, P, Abgottspon, D, Hutter, A, Scharenberg, M, Jian, X, Navarra, G, Rabbani, S, Smiesko, M, Luedin, N, Jakob, R.P, Schwardt, O, Maier, T, Sharpe, T, Ernst, B. | | Deposit date: | 2014-03-10 | | Release date: | 2015-02-25 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Fimh Antagonists: Bioisosteres to Improve the in Vitro and in Vivo Pk/Pd Profile.
J.Med.Chem., 58, 2015
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4CSS
 | | Crystal structure of FimH in complex with a sulfonamide biphenyl alpha D-mannoside | | Descriptor: | 4'-(alpha-D-Mannopyranosyloxy)-biphenyl-4-methyl sulfonamide, GLYCEROL, PROTEIN FIMH | | Authors: | Kleeb, S, Pang, L, Mayer, K, Sigl, A, Eris, D, Preston, R.C, Zihlmann, P, Abgottspon, D, Hutter, A, Scharenberg, M, Jian, X, Navarra, G, Rabbani, S, Smiesko, M, Luedin, N, Jakob, R.P, Schwardt, O, Maier, T, Sharpe, T, Ernst, B. | | Deposit date: | 2014-03-10 | | Release date: | 2015-02-25 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (1.069 Å) | | Cite: | Fimh Antagonists: Bioisosteres to Improve the in Vitro and in Vivo Pk/Pd Profile.
J.Med.Chem., 58, 2015
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1M6K
 | | Structure of the OXA-1 class D beta-lactamase | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, beta-lactamase OXA-1 | | Authors: | Sun, T, Nukaga, M, Mayama, K, Braswell, E.H, Knox, J.R. | | Deposit date: | 2002-07-16 | | Release date: | 2003-01-14 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Comparison of beta-lactamases of classes A and D: 1.5A crystallographic structure of the class D OXA-1 oxacillinase
PROTEIN SCI., 12, 2003
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1N9B
 | | Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, BETA-LACTAMASE SHV-2, ... | | Authors: | Nukaga, M, Mayama, K, Hujer, A.M, Bonomo, R.A, Knox, J.R. | | Deposit date: | 2002-11-22 | | Release date: | 2003-04-08 | | Last modified: | 2023-08-16 | | Method: | X-RAY DIFFRACTION (0.9 Å) | | Cite: | Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme
J.Mol.Biol., 328, 2003
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3VIQ
 | | Crystal structure of Swi5-Sfr1 complex from fission yeast | | Descriptor: | GLYCEROL, Mating-type switching protein swi5, NITRATE ION, ... | | Authors: | Kuwabara, N, Murayama, Y, Hashimoto, H, Kokabu, Y, Ikeguchi, M, Sato, M, Mayanagi, K, Tsutsui, Y, Iwasaki, H, Shimizu, T. | | Deposit date: | 2011-10-06 | | Release date: | 2012-08-22 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Mechanistic insights into the activation of Rad51-mediated strand exchange from the structure of a recombination activator, the Swi5-Sfr1 complex
Structure, 20, 2012
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1HZO
 | | STRUCTURE OF CLASS A CEPHALOSPORINASE FROM PROTEUS VULGARIS K1 | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, BETA-LACTAMASE | | Authors: | Nukaga, M, Crichlow, G.V, Kuzin, A.P, Mayama, K, Knox, J.R. | | Deposit date: | 2001-01-25 | | Release date: | 2002-04-03 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Structure of an extended-spectrum class A beta-lactamase from Proteus vulgaris K1.
J.Mol.Biol., 317, 2002
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