6JTB
 
 | | Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate from Porphyromonas gingivalis (Space) | | Descriptor: | Asp/Glu-specific dipeptidyl-peptidase, CITRIC ACID, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Sakamoto, Y, Suzuki, Y, Iizuka, I, Roppongi, S, Kushibiki, C, Nakamura, A, Ogasawara, W, Tanaka, N. | | Deposit date: | 2019-04-10 | | Release date: | 2019-10-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase.
Sci Rep, 9, 2019
|
|
6JTC
 | | Crystal structure of dipeptidyl peptidase 11 (DPP11) with SH-5 from Porphyromonas gingivalis (Space) | | Descriptor: | 2-(2-azanylethylamino)-5-nitro-benzoic acid, Asp/Glu-specific dipeptidyl-peptidase, GLYCEROL | | Authors: | Sakamoto, Y, Suzuki, Y, Iizuka, I, Roppongi, S, Kushibiki, C, Nakamura, A, Ogasawara, W, Tanaka, N. | | Deposit date: | 2019-04-10 | | Release date: | 2019-10-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.39 Å) | | Cite: | Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase.
Sci Rep, 9, 2019
|
|
6KIL
 | | N21Q mutant thioredoxin from Halobacterium salinarum NRC-1 | | Descriptor: | Thioredoxin | | Authors: | Arai, S, Shibazaki, C, Shimizu, R, Adachi, M, Ishibashi, M, Tokunaga, H, Tokunaga, M. | | Deposit date: | 2019-07-19 | | Release date: | 2020-01-15 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Catalytic mechanism and evolutional characteristics of thioredoxin from Halobacterium salinarum NRC-1.
Acta Crystallogr.,Sect.D, 76, 2020
|
|
6L9C
 | | Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 | | Descriptor: | COPPER (II) ION, Phenylethylamine oxidase, SODIUM ION | | Authors: | Murakawa, T, Kurihara, K, Shoji, M, Shibazaki, C, Sunami, T, Tamada, T, Yano, N, Yamada, T, Kusaka, K, Suzuki, M, Shigeta, Y, Kuroki, R, Hayashi, H, Yano, Y, Tanizawa, K, Adachi, M, Okajima, T. | | Deposit date: | 2019-11-08 | | Release date: | 2020-04-29 | | Last modified: | 2023-11-22 | | Method: | NEUTRON DIFFRACTION (1.14 Å), X-RAY DIFFRACTION | | Cite: | Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing.
Proc.Natl.Acad.Sci.USA, 117, 2020
|
|
1LZV
 | | Site-Specific Mutant (Tyr7 replaced with His) of Human Carbonic Anhydrase II | | Descriptor: | Carbonic Anhydrase II, ZINC ION | | Authors: | Tu, C.K, Qian, M, An, H, Wadhwa, N.R, Duda, D.M, Yoshioka, C, Pathak, Y, McKenna, R, Laipis, P.J, Silverman, D.N. | | Deposit date: | 2002-06-11 | | Release date: | 2002-10-23 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Kinetic analysis of multiple proton shuttles in the active site of human carbonic anhydrase.
J.Biol.Chem., 277, 2002
|
|
1TB0
 | | Effect of Shuttle Location and pH Environment on H+ Transfer in Human Carbonic Anhydrase II | | Descriptor: | CHLORIDE ION, Carbonic anhydrase II, ZINC ION | | Authors: | Fisher, Z, Hernandez Prada, J.A, Tu, C, Duda, D, Yoshioka, C, An, H, Govindasamy, L, Silverman, D.N, McKenna, R. | | Deposit date: | 2004-05-19 | | Release date: | 2005-01-25 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural and kinetic characterization of active-site histidine as a proton shuttle in catalysis by human carbonic anhydrase II.
Biochemistry, 44, 2005
|
|
1OI7
 | | The Crystal Structure of Succinyl-CoA synthetase alpha subunit from Thermus Thermophilus | | Descriptor: | SUCCINYL-COA SYNTHETASE ALPHA CHAIN | | Authors: | Takahashi, H, Tokunaga, Y, Kuroishi, C, Babayeva, N, Kuramitsu, S, Yokoyama, S, Miyano, M, Tahirov, T.H. | | Deposit date: | 2003-06-10 | | Release date: | 2003-07-04 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (1.23 Å) | | Cite: | The Crystal Structure of Succinyl-Coa Synthetase from Thermus Thermophilus
To be Published
|
|
1Q5D
 | | Epothilone B-bound Cytochrome P450epoK | | Descriptor: | 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE, P450 epoxidase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nagano, S, Li, H, Shimizu, H, Nishida, C, Ogura, H, Ortiz de Montellano, P.R, Poulos, T.L. | | Deposit date: | 2003-08-06 | | Release date: | 2003-10-28 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Crystal structures of epothilone D-bound, epothilone B-bound, and substrate-free forms of cytochrome P450epoK
J.Biol.Chem., 278, 2003
|
|
1Q5E
 | | Substrate-free Cytochrome P450epoK | | Descriptor: | P450 epoxidase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nagano, S, Li, H, Shimizu, H, Nishida, C, Ogura, H, Ortiz de Montellano, P.R, Poulos, T.L. | | Deposit date: | 2003-08-06 | | Release date: | 2003-10-28 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | Crystal structures of epothilone D-bound, epothilone B-bound, and substrate-free forms of cytochrome P450epoK
J.Biol.Chem., 278, 2003
|
|
1J2E
 | | Crystal structure of Human Dipeptidyl peptidase IV | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Dipeptidyl peptidase IV | | Authors: | Hiramatsu, H, Kyono, K, Higashiyama, Y, Fukushima, C, Shima, H, Sugiyama, S, Inaka, K, Yamamoto, A, Shimizu, R. | | Deposit date: | 2002-12-30 | | Release date: | 2003-12-30 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | The structure and function of human dipeptidyl peptidase IV, possessing a unique eight-bladed beta-propeller fold.
Biochem.Biophys.Res.Commun., 302, 2003
|
|
1PKF
 | | Crystal Structure of Epothilone D-bound Cytochrome P450epoK | | Descriptor: | EPOTHILONE D, PROTOPORPHYRIN IX CONTAINING FE, cytochrome p450EpoK | | Authors: | Nagano, S, Li, H, Shimizu, H, Nishida, C, Ogura, H, Ortiz de Montellano, P.R, Poulos, T.L. | | Deposit date: | 2003-06-05 | | Release date: | 2003-10-28 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal Structures of Epothilone D-bound, Epothilone B-bound, and Substrate-free Forms of Cytochrome P450epoK
J.Biol.Chem., 278, 2003
|
|
1TBT
 | | Effect of Shuttle Location and pH Environment on H+ Transfer in Human Carbonic Anhydrase II | | Descriptor: | Carbonic anhydrase II, ZINC ION | | Authors: | Fisher, Z, Hernandez Prada, J.A, Tu, C.K, Duda, D, Yoshioka, C, An, H, Govindasamy, L, Silverman, D.N, McKenna, R. | | Deposit date: | 2004-05-20 | | Release date: | 2005-01-25 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural and Kinetic Characterization of Active-Site Histidine as a Proton Shuttle in Catalysis by Human Carbonic Anhydrase II.
Biochemistry, 44, 2005
|
|
7D9Z
 | | Crystal structure of anti-basigin Fab fragment | | Descriptor: | 1,2-ETHANEDIOL, CITRATE ANION, Heavy chain of antibody Fab fragment, ... | | Authors: | Sakuragi, T, Kanai, R, Narita, H, Onishi, E, Miyazaki, T, Baba, T, Nakagawa, A, Toyoshima, C, Nagata, S. | | Deposit date: | 2020-10-14 | | Release date: | 2021-10-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.123 Å) | | Cite: | The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes.
Nat.Struct.Mol.Biol., 28, 2021
|
|
7DCE
 | | Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment | | Descriptor: | 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, Heavy chain of Fab fragment, Isoform 2 of Basigin, ... | | Authors: | Sakuragi, T, Kanai, R, Tsutsumi, A, Narita, H, Onishi, E, Miyazaki, T, Baba, T, Nakagawa, A, Kikkawa, M, Toyoshima, C, Nagata, S. | | Deposit date: | 2020-10-26 | | Release date: | 2021-10-20 | | Last modified: | 2024-01-24 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes.
Nat.Struct.Mol.Biol., 28, 2021
|
|
7DKD
 | | Stenotrophomonas maltophilia DPP7 in complex with Asn-Tyr | | Descriptor: | ASPARAGINE, Dipeptidyl-peptidase, GLYCEROL, ... | | Authors: | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | Deposit date: | 2020-11-23 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
|
|
7DKC
 | | Stenotrophomonas maltophilia DPP7 in complex with Tyr-Tyr | | Descriptor: | Dipeptidyl-peptidase, GLYCEROL, TYROSINE | | Authors: | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | Deposit date: | 2020-11-23 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
|
|
7DKE
 | | Stenotrophomonas maltophilia DPP7 in complex with Phe-Tyr | | Descriptor: | Dipeptidyl-peptidase, GLYCEROL, PHENYLALANINE, ... | | Authors: | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | Deposit date: | 2020-11-23 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.91 Å) | | Cite: | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
|
|
7DKB
 | | Stenotrophomonas maltophilia DPP7 in complex with Val-Tyr | | Descriptor: | Dipeptidyl-peptidase, TYROSINE, VALINE | | Authors: | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | Deposit date: | 2020-11-23 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.03 Å) | | Cite: | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
|
|
8HE5
 | | RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome | | Descriptor: | DNA (198-MER), DNA repair protein, DNA-directed RNA polymerase subunit, ... | | Authors: | Osumi, K, Kujirai, T, Ehara, H, Kinoshita, C, Saotome, M, Kagawa, W, Sekine, S, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2022-11-07 | | Release date: | 2023-07-05 | | Method: | ELECTRON MICROSCOPY (6.95 Å) | | Cite: | Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome.
J.Mol.Biol., 435, 2023
|
|
7DAA
 | | Crystal structure of basigin complexed with anti-basigin Fab fragment | | Descriptor: | CADMIUM ION, Heavy chain of antibody Fab fragment, Isoform 2 of Basigin, ... | | Authors: | Sakuragi, T, Kanai, R, Narita, H, Onishi, E, Miyazaki, T, Baba, T, Nakagawa, A, Toyoshima, C, Nagata, S. | | Deposit date: | 2020-10-16 | | Release date: | 2021-10-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.51 Å) | | Cite: | The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes.
Nat.Struct.Mol.Biol., 28, 2021
|
|
3J2V
 | | CryoEM structure of HBV core | | Descriptor: | PreC/core protein | | Authors: | Yu, X, Jin, L, Jih, J, Shih, C, Zhou, Z.H. | | Deposit date: | 2013-01-11 | | Release date: | 2013-10-02 | | Last modified: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | 3.5 angstrom cryoEM Structure of Hepatitis B Virus Core Assembled from Full-Length Core Protein.
Plos One, 8, 2013
|
|
1R15
 | | Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P | | Descriptor: | ADP-ribosyl cyclase, ANY 5'-MONOPHOSPHATE NUCLEOTIDE, NICOTINAMIDE | | Authors: | Love, M.L, Szebenyi, D.M.E, Kriksunov, I.A, Thiel, D.J, Munshi, C, Graeff, R, Lee, H.C, Hao, Q. | | Deposit date: | 2003-09-23 | | Release date: | 2004-03-09 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | ADP-ribosyl cyclase; crystal structures reveal a covalent intermediate.
Structure, 12, 2004
|
|
7X7I
 | | Ancestral L-Lys oxidase (AncLLysO-2) ligand free form | | Descriptor: | FAD dependent enzyme, FLAVIN-ADENINE DINUCLEOTIDE | | Authors: | Motoyama, T, Ishida, C, Hasebe, F, Ito, S, Nakano, S. | | Deposit date: | 2022-03-09 | | Release date: | 2023-01-18 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis
Acs Omega, 7, 2022
|
|
7X7J
 | | Ancestral L-Lys oxidase (AncLLysO-2) L-Lys binding form | | Descriptor: | FAD dependent enzyme, FLAVIN-ADENINE DINUCLEOTIDE, LYSINE | | Authors: | Motoyama, T, Ishida, C, Hasebe, F, Ito, S, Nakano, S. | | Deposit date: | 2022-03-09 | | Release date: | 2023-01-18 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis
Acs Omega, 7, 2022
|
|
5IPT
 | | Cryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV-bound conformation, state 5 | | Descriptor: | Ionotropic glutamate receptor subunit NR2B, N-methyl-D-aspartate receptor subunit NR1-8a | | Authors: | Zhu, S, Stein, A.R, Yoshioka, C, Lee, C.H, Goehring, A, Mchaourab, S.H, Gouaux, E. | | Deposit date: | 2016-03-09 | | Release date: | 2016-04-20 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (14.1 Å) | | Cite: | Mechanism of NMDA Receptor Inhibition and Activation.
Cell, 165, 2016
|
|
