Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help
Search by PDB author
4WJ3
DownloadVisualize
BU of 4wj3 by Molmil
Crystal structure of the asparagine transamidosome from Pseudomonas aeruginosa
Descriptor: 76mer-tRNA, Aspartate--tRNA(Asp/Asn) ligase, Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, ...
Authors:Suzuki, T, Nakamura, A, Kato, K, Tanaka, I, Yao, M.
Deposit date:2014-09-29
Release date:2014-12-31
Last modified:2020-02-05
Method:X-RAY DIFFRACTION (3.705 Å)
Cite:Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis
Proc.Natl.Acad.Sci.USA, 112, 2015
3SSI
DownloadVisualize
BU of 3ssi by Molmil
PROTEINASE INHIBITOR SSI (STREPTOMYCES SUBTILISIN, INHIBITOR) FROM STREPTOMYCES ALBOGRISEOLUS
Descriptor: STREPTOMYCES SUBTILISIN INHIBITOR
Authors:Suzuki, T, Nonaka, T, Mitsui, Y.
Deposit date:1996-03-01
Release date:1996-08-17
Last modified:2024-06-05
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural Modulation of the Protein Proteinase Inhibitor Ssi (Streptomyces Subtilisin Inhibitor)
To be Published
5UD5
DownloadVisualize
BU of 5ud5 by Molmil
Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase bound to tRNA(Pyl)
Descriptor: Pyrrolysine--tRNA ligase, RNA (70-MER), ZINC ION
Authors:Suzuki, T, Soll, D.
Deposit date:2016-12-23
Release date:2017-10-11
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.347 Å)
Cite:Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase.
Nat. Chem. Biol., 13, 2017
5V6X
DownloadVisualize
BU of 5v6x by Molmil
Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase mutant (32A NTD) bound to tRNA(Pyl)
Descriptor: Pyrrolysine--tRNA ligase, RNA (70-MER), ZINC ION
Authors:Suzuki, T, Soll, D.
Deposit date:2017-03-17
Release date:2017-10-11
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.76 Å)
Cite:Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase.
Nat. Chem. Biol., 13, 2017
4WJ4
DownloadVisualize
BU of 4wj4 by Molmil
Crystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid
Descriptor: 76mer-tRNA, ASPARTIC ACID, Aspartate--tRNA(Asp/Asn) ligase
Authors:Suzuki, T, Nakamura, A, Kato, K, Tanaka, I, Yao, M.
Deposit date:2014-09-29
Release date:2014-12-31
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (3.294 Å)
Cite:Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis
Proc.Natl.Acad.Sci.USA, 112, 2015
6KTQ
DownloadVisualize
BU of 6ktq by Molmil
Crystal structure of catalytic domain of homocitrate synthase from Sulfolobus acidocaldarius (SaHCS(dRAM)) in complex with alpha-ketoglutarate/Zn2+/CoA
Descriptor: 2-OXOGLUTARIC ACID, COENZYME A, Homocitrate synthase, ...
Authors:Suzuki, T, Tomita, T, Kuzuyama, T, Nishiyama, M.
Deposit date:2019-08-28
Release date:2020-09-02
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.98 Å)
Cite:Involvement of subdomain II in the recognition of acetyl-CoA revealed by the crystal structure of homocitrate synthase from Sulfolobus acidocaldarius.
Febs J., 288, 2021
7CSL
DownloadVisualize
BU of 7csl by Molmil
Crystal structure of the archaeal EF1A-EF1B complex
Descriptor: Elongation factor 1-alpha, Elongation factor 1-beta
Authors:Suzuki, T, Ito, K, Miyoshi, T, Murakami, R, Uchiumi, T.
Deposit date:2020-08-15
Release date:2021-06-23
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural insights into the Switching Off of the Interaction between the Archaeal Ribosomal Stalk and aEF1A by Nucleotide Exchange Factor aEF1B.
J.Mol.Biol., 433, 2021
8IB1
DownloadVisualize
BU of 8ib1 by Molmil
Structure of the LAH31 Fab bound to an influenza virus HA epitope peptide
Descriptor: Hemagglutinin HA2 chain, LAH31 Fab heavy chain, LAH31 Fab light chain
Authors:Suzuki, T, Hashiguchi, T.
Deposit date:2023-02-09
Release date:2023-07-26
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Structural basis for cross-group recognition of an influenza virus hemagglutinin antibody that targets postfusion stabilized epitope.
Plos Pathog., 19, 2023
7XWA
DownloadVisualize
BU of 7xwa by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Suzuki, T, Kimura, K, Hashiguchi, T.
Deposit date:2022-05-26
Release date:2022-09-28
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.36 Å)
Cite:Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5.
Cell, 185, 2022
3WLU
DownloadVisualize
BU of 3wlu by Molmil
Crystal Structure of human galectin-9 NCRD with Selenolactose
Descriptor: 2-(trimethylsilyl)ethyl 4-O-beta-D-galactopyranosyl-6-Se-methyl-6-seleno-beta-D-glucopyranoside, Galectin-9
Authors:Makyio, H, Suzuki, T, Ando, H, Yamada, Y, Ishida, H, Kiso, M, Wakatsuki, S, Kato, R.
Deposit date:2013-11-14
Release date:2014-11-05
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Expanded potential of seleno-carbohydrates as a molecular tool for X-ray structural determination of a carbohydrate-protein complex with single/multi-wavelength anomalous dispersion phasing
Bioorg.Med.Chem., 22, 2014
8HU1
DownloadVisualize
BU of 8hu1 by Molmil
E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and ct6A37 in classical state
Descriptor: 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ...
Authors:Akiyama, N, Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T.
Deposit date:2022-12-22
Release date:2024-04-03
Last modified:2024-06-05
Method:ELECTRON MICROSCOPY (2.69 Å)
Cite:Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine.
Nat.Struct.Mol.Biol., 31, 2024
8HTZ
DownloadVisualize
BU of 8htz by Molmil
E. coli 70S ribosome complexed with H. marismortui tRNA_Ile2 bearing agm2C34 in classical state
Descriptor: 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ...
Authors:Akiyama, N, Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T.
Deposit date:2022-12-22
Release date:2024-04-03
Last modified:2024-06-05
Method:ELECTRON MICROSCOPY (2.4 Å)
Cite:Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine.
Nat.Struct.Mol.Biol., 31, 2024
8HSP
DownloadVisualize
BU of 8hsp by Molmil
E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and t6A37 in classical state
Descriptor: 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ...
Authors:Akiyama, N, Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T.
Deposit date:2022-12-20
Release date:2024-04-03
Last modified:2024-06-05
Method:ELECTRON MICROSCOPY (2.32 Å)
Cite:Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine.
Nat.Struct.Mol.Biol., 31, 2024
8IF2
DownloadVisualize
BU of 8if2 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BQ.1.1 variant spike protein in complex with its receptor ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Kimura, K, Suzuki, T, Hashiguchi, T.
Deposit date:2023-02-17
Release date:2023-05-17
Last modified:2023-05-24
Method:X-RAY DIFFRACTION (2.78 Å)
Cite:Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.
Nat Commun, 14, 2023
2VQF
DownloadVisualize
BU of 2vqf by Molmil
Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding
Descriptor: 16S RRNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ...
Authors:Kurata, S, Weixlbaumer, A, Ohtsuki, T, Shimazaki, T, Wada, T, Kirino, Y, Takai, K, Watanabe, K, Ramakrishnan, V, Suzuki, T.
Deposit date:2008-03-14
Release date:2008-04-29
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding.
J.Biol.Chem., 283, 2008
2VQE
DownloadVisualize
BU of 2vqe by Molmil
Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding
Descriptor: 16S RRNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ...
Authors:Kurata, S, Weixlbaumer, A, Ohtsuki, T, Shimazaki, T, Wada, T, Kirino, Y, Takai, K, Watanabe, K, Ramakrishnan, V, Suzuki, T.
Deposit date:2008-03-13
Release date:2008-04-29
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding.
J.Biol.Chem., 283, 2008
5Y5N
DownloadVisualize
BU of 5y5n by Molmil
Crystal structure of human Sirtuin 2 in complex with a selective inhibitor
Descriptor: 2-[[3-(2-phenylethoxy)phenyl]amino]benzamide, NAD-dependent protein deacetylase sirtuin-2, ZINC ION
Authors:Mellini, P, Itoh, Y, Tsumoto, H, Li, Y, Suzuki, M, Tokuda, N, Kakizawa, T, Miura, Y, Takeuchi, J, Lahtela-Kakkonen, M, Suzuki, T.
Deposit date:2017-08-09
Release date:2017-09-06
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Potent mechanism-based sirtuin-2-selective inhibition by anin situ-generated occupant of the substrate-binding site, "selectivity pocket" and NAD+-binding site.
Chem Sci, 8, 2017
3DJN
DownloadVisualize
BU of 3djn by Molmil
Crystal structure of mouse TIS21
Descriptor: Protein BTG2
Authors:Yang, X, Morita, M, Wang, H, Suzuki, T, Bartlam, M, Yamamoto, T.
Deposit date:2008-06-24
Release date:2008-11-11
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structures of human BTG2 and mouse TIS21 involved in suppression of CAF1 deadenylase activity
Nucleic Acids Res., 36, 2008
5GVO
DownloadVisualize
BU of 5gvo by Molmil
Solution NMR structure of a new lasso peptide sphaericin
Descriptor: Uncharacterized protein
Authors:Hemmi, H, Kodani, S, Inoue, Y, Suzuki, M, Dohra, H, Suzuki, T, Ohnishi-Kameyama, M.
Deposit date:2016-09-06
Release date:2017-04-05
Method:SOLUTION NMR
Cite:Sphaericin, a Lasso Peptide from the Rare Actinomycete Planomonospora sphaerica
Eur.J.Org.Chem., 2017
7VNW
DownloadVisualize
BU of 7vnw by Molmil
Crystal Structure of tRNAVal from Sulfolobus Tokodaii(Dephosphorylated)
Descriptor: RNA (78-MER)
Authors:Yamashita, S, Ohira, T, Suzuki, T, Tomtia, K.
Deposit date:2021-10-12
Release date:2022-05-04
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (2.61 Å)
Cite:Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.
Nature, 605, 2022
7VNX
DownloadVisualize
BU of 7vnx by Molmil
Crystal structure of TkArkI
Descriptor: GUANOSINE, TkArkI
Authors:Yamashita, S, Minowa, K, Ohira, T, Suzuki, T, Tomita, K.
Deposit date:2021-10-12
Release date:2022-05-04
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.801 Å)
Cite:Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.
Nature, 605, 2022
7VNV
DownloadVisualize
BU of 7vnv by Molmil
Crystal Structure of tRNAVal from Sulfolobus Tokodaii
Descriptor: RNA (78-MER)
Authors:Yamashita, S, Ohira, T, Suzuki, T, Tomtia, K.
Deposit date:2021-10-12
Release date:2022-05-04
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.
Nature, 605, 2022
3DJU
DownloadVisualize
BU of 3dju by Molmil
Crystal structure of human BTG2
Descriptor: Protein BTG2
Authors:Yang, X, Morita, M, Wang, H, Suzuki, T, Bartlam, M, Yamamoto, T.
Deposit date:2008-06-24
Release date:2008-11-11
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.26 Å)
Cite:Crystal structures of human BTG2 and mouse TIS21 involved in suppression of CAF1 deadenylase activity
Nucleic Acids Res., 36, 2008
8HGM
DownloadVisualize
BU of 8hgm by Molmil
Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-11 Fab heavy chain, NIV-11 Fab light chain, ...
Authors:Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y.
Deposit date:2022-11-15
Release date:2023-10-25
Last modified:2024-09-25
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
8HGL
DownloadVisualize
BU of 8hgl by Molmil
SARS-CoV-2 spike in complex with neutralizing antibody NIV-11
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-11 Fab heavy chain, ...
Authors:Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y.
Deposit date:2022-11-15
Release date:2023-10-25
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023

225399

PDB entries from 2024-09-25

PDB statisticsPDBj update infoContact PDBjnumon