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6UAN
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BU of 6uan by Molmil
B-Raf:14-3-3 complex
Descriptor: 14-3-3 zeta, Serine/threonine-protein kinase B-raf
Authors:Kondo, Y, Ognjenovic, J, Banerjee, S, Karandur, D, Merk, A, Kulhanek, K, Wong, K, Roose, J.P, Subramaniam, S, Kuriyan, J.
Deposit date:2019-09-11
Release date:2019-09-25
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:Cryo-EM structure of a dimeric B-Raf:14-3-3 complex reveals asymmetry in the active sites of B-Raf kinases.
Science, 366, 2019
4PJO
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BU of 4pjo by Molmil
Minimal U1 snRNP
Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CHLORIDE ION, ETHANOL, ...
Authors:Kondo, Y, Oubridge, C, van Roon, A.M, Nagai, K.
Deposit date:2014-05-12
Release date:2014-12-31
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.
Elife, 4, 2015
6AXF
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BU of 6axf by Molmil
Structure of RasGRP2 in complex with Rap1B
Descriptor: RAS guanyl-releasing protein 2, Ras-related protein Rap-1b
Authors:Kondo, Y, Iwig, J.S, Kuriyan, J.
Deposit date:2017-09-06
Release date:2017-10-11
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:A histidine pH sensor regulates activation of the Ras-specific guanine nucleotide exchange factor RasGRP1.
Elife, 6, 2017
6AXG
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BU of 6axg by Molmil
Structure of RasGRP4 in complex with HRas
Descriptor: GTPase HRas, RAS guanyl-releasing protein 4
Authors:Kondo, Y, Iwig, J.S, Kuriyan, J.
Deposit date:2017-09-06
Release date:2017-10-11
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (3.302 Å)
Cite:A histidine pH sensor regulates activation of the Ras-specific guanine nucleotide exchange factor RasGRP1.
Elife, 6, 2017
4PKD
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BU of 4pkd by Molmil
U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2
Descriptor: IMIDAZOLE, MAGNESIUM ION, U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein 70 kDa, ...
Authors:Oubridge, C, Kondo, Y, van Roon, A.M, Nagai, K.
Deposit date:2014-05-14
Release date:2014-12-31
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.
Elife, 4, 2015
5WDS
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BU of 5wds by Molmil
Choanoflagellate Salpingoeca rosetta Ras with GDP bound
Descriptor: GLYCEROL, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ...
Authors:Kondo, Y, Gee, C.L, Kuriyan, J.
Deposit date:2017-07-05
Release date:2017-07-19
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Deconstruction of the Ras switching cycle through saturation mutagenesis.
Elife, 6, 2017
5WDR
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BU of 5wdr by Molmil
Choanoflagellate Salpingoeca rosetta Ras with GMP-PNP
Descriptor: MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, Ras protein, ...
Authors:Kondo, Y, Gee, C.L, Kuriyan, J.
Deposit date:2017-07-05
Release date:2017-07-19
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Deconstruction of the Ras switching cycle through saturation mutagenesis.
Elife, 6, 2017
2RT8
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BU of 2rt8 by Molmil
Structure of metallo-dna in solution
Descriptor: DNA (5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'), MERCURY (II) ION
Authors:Yamaguchi, H, Sebera, J, Kondo, J, Oda, S, Komuro, T, Kawamura, T, Dairaku, T, Kondo, Y, Okamoto, I, Ono, A, Burda, J.V, Kojima, C, Sychrovsky, V, Tanaka, Y.
Deposit date:2013-06-18
Release date:2014-03-05
Last modified:2023-06-14
Method:SOLUTION NMR
Cite:The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation.
Nucleic Acids Res., 42, 2014
2RVP
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BU of 2rvp by Molmil
Solution structure of DNA Containing Metallo-Base-Pair
Descriptor: DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'), DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), SILVER ION
Authors:Dairaku, T, Furuita, K, Sato, H, Sebera, J, Nakashima, K, Kondo, J, Yamanaka, D, Kondo, Y, Okamoto, I, Ono, A, Sychrovsky, V, Kojima, C, Tanaka, Y.
Deposit date:2016-03-22
Release date:2016-08-31
Last modified:2023-06-14
Method:SOLUTION NMR
Cite:Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.
Chemistry, 22, 2016
3SI8
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BU of 3si8 by Molmil
Human DNA polymerase eta - DNA ternary complex with the 5'T of a CPD in the active site (TT2)
Descriptor: (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol, 1,2-ETHANEDIOL, 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, ...
Authors:Biertumpfel, C, Zhao, Y, Kondo, Y, Ramon-Maiques, S, Gregory, M, Lee, J.Y, Masutani, C, Lehmann, A.R, Hanaoka, F, Yang, W.
Deposit date:2011-06-17
Release date:2011-08-03
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Structure and mechanism of human DNA polymerase eta.
Nature, 465, 2010
5DZL
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BU of 5dzl by Molmil
Crystal structure of the protein human CEACAM1
Descriptor: Carcinoembryonic antigen-related cell adhesion molecule 1
Authors:Huang, Y.H, Russell, A, Gandhi, A.K, Kondo, Y, Chen, Q, Petsko, G.A, Blumberg, R.S.
Deposit date:2015-09-25
Release date:2015-10-07
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (3.4006 Å)
Cite:CEACAM1 regulates TIM-3-mediated tolerance and exhaustion.
Nature, 517, 2015
4QXW
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BU of 4qxw by Molmil
Crystal structure of the human CEACAM1 membrane distal amino terminal (N)-domain
Descriptor: Carcinoembryonic antigen-related cell adhesion molecule 1, MALONIC ACID, octyl beta-D-glucopyranoside
Authors:Huang, Y.H, Gandhi, A.K, Russell, A, Kondo, Y, Chen, Q, Petsko, G.A, Blumberg, R.S.
Deposit date:2014-07-22
Release date:2014-11-12
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.04 Å)
Cite:CEACAM1 regulates TIM-3-mediated tolerance and exhaustion.
Nature, 517, 2015
4TWT
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BU of 4twt by Molmil
Human TNFa dimer in complex with the semi-synthetic bicyclic peptide M21
Descriptor: (2,4,6-trimethylbenzene-1,3,5-triyl)trimethanol, ALA-CYS-PRO-PRO-CYS-LEU-TRP-GLN-VAL-LEU-CYS-GLY, GLYCEROL, ...
Authors:Luzi, S, Kondo, Y, Bernard, E, Stadler, L, Winter, G, Holliger, P.
Deposit date:2014-07-01
Release date:2015-02-04
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (2.85 Å)
Cite:Subunit disassembly and inhibition of TNF alpha by a semi-synthetic bicyclic peptide.
Protein Eng.Des.Sel., 28, 2015
4P3K
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BU of 4p3k by Molmil
Structure of ancestral PyrR protein (PLUMPyrR)
Descriptor: Ancestral PyrR protein (Plum), PENTAETHYLENE GLYCOL, SODIUM ION, ...
Authors:Perica, T, Kondo, Y, Tiwari, S, McLaughlin, S, Steward, A, Reuter, N, Clarke, J, Teichmann, S.A.
Deposit date:2014-03-08
Release date:2014-12-17
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Science, 346, 2014
4P80
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BU of 4p80 by Molmil
Structure of ancestral PyrR protein (AncGREENPyrR)
Descriptor: Ancestral PyrR protein (Green), SULFATE ION
Authors:Perica, T, Kondo, Y, Tiwari, S, McLaughlin, S, Steward, A, Reuter, N, Clarke, J, Teichmann, S.A.
Deposit date:2014-03-29
Release date:2014-12-17
Last modified:2014-12-31
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Science, 346, 2014
4P81
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BU of 4p81 by Molmil
Structure of ancestral PyrR protein (AncORANGEPyrR)
Descriptor: Ancestral PyrR protein (Orange), GLYCEROL, SULFATE ION
Authors:Perica, T, Kondo, Y, Tiwari, S, McLaughlin, S, Steward, A, Reuter, N, Clarke, J, Teichmann, S.A.
Deposit date:2014-03-29
Release date:2014-12-17
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Science, 346, 2014
4P82
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BU of 4p82 by Molmil
Structure of PyrR protein from Bacillus subtilis
Descriptor: Bifunctional protein PyrR, SULFATE ION
Authors:Perica, T, Kondo, Y, Tiwari, S, McLaughlin, S, Steward, A, Reuter, N, Clarke, J, Teichmann, S.A.
Deposit date:2014-03-30
Release date:2014-12-17
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Science, 346, 2014
4P83
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BU of 4p83 by Molmil
Structure of engineered PyrR protein (PURPLE PyrR)
Descriptor: Engineered PyrR protein (Purple), URIDINE-5'-MONOPHOSPHATE
Authors:Perica, T, Kondo, Y, Tiwari, S, McLaughlin, S, Steward, A, Reuter, N, Clarke, J, Teichmann, S.A.
Deposit date:2014-03-30
Release date:2014-12-17
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Science, 346, 2014
4P86
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BU of 4p86 by Molmil
Structure of PyrR protein from Bacillus subtilis with GMP
Descriptor: Bifunctional protein PyrR, GLYCEROL, GUANOSINE-5'-MONOPHOSPHATE
Authors:Perica, T, Kondo, Y, Tiwari, S, McLaughlin, S, Steward, A, Reuter, N, Clarke, J, Teichmann, S.A.
Deposit date:2014-03-30
Release date:2014-12-17
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Science, 346, 2014
4P84
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BU of 4p84 by Molmil
Structure of engineered PyrR protein (VIOLET PyrR)
Descriptor: Bifunctional protein PyrR, GLYCEROL, SULFATE ION
Authors:Perica, T, Kondo, Y, Tiwari, S, McLaughlin, S, Steward, A, Reuter, N, Clarke, J, Teichmann, S.A.
Deposit date:2014-03-30
Release date:2014-12-17
Last modified:2023-12-20
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Science, 346, 2014
6K55
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BU of 6k55 by Molmil
Inactivated mutant (D140A) of Hyperthermophilic GH6 cellobiohydrolase II (HmCel6A) in complex with hexasaccharide
Descriptor: Glucanase, MAGNESIUM ION, beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
Authors:Baba, S, Takeda, M, Okuma, J, Hirose, Y, Nishimura, A, Takata, M, Oda, K, Shibata, D, Kondo, Y, Kumasaka, T.
Deposit date:2019-05-28
Release date:2020-06-03
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.883 Å)
Cite:A hyperthermophilic cellobiohydrolase mined from a hot spring metagenomic data
To Be Published
6K53
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BU of 6k53 by Molmil
A variant of metagenome-derived GH6 cellobiohydrolase, HmCel6A (P88S/L230F/F414S)
Descriptor: CITRATE ANION, GH6 cellobiohydrolase, HMCEL6A, ...
Authors:Baba, S, Takeda, M, Okuma, J, Hirose, Y, Nishimura, A, Takata, M, Oda, K, Shibata, D, Kondo, Y, Kumasaka, T.
Deposit date:2019-05-28
Release date:2020-06-03
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:A hyperthermophilic GH6 cellobiohydrolase (HmCel6A) from a hot spring metagenomic data
To Be Published
6K54
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BU of 6k54 by Molmil
Hyperthermophilic GH6 cellobiohydrolase II (HmCel6A) in complex with trisaccharide
Descriptor: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL, CALCIUM ION, DI(HYDROXYETHYL)ETHER, ...
Authors:Baba, S, Takeda, M, Okuma, J, Hirose, Y, Nishimura, A, Takata, M, Oda, K, Shibata, D, Kondo, Y, Kumasaka, T.
Deposit date:2019-05-28
Release date:2020-06-03
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.905 Å)
Cite:Novel hyperthermophilic cellobiohydrolase II isolated from hot spring microbial community
To Be Published
6K52
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BU of 6k52 by Molmil
Hyperthermophilic GH6 cellobiohydrolase (HmCel6A) from the microbial flora of a Japanese hot spring
Descriptor: ACETATE ION, CALCIUM ION, GH6 cellobiohydrolase, ...
Authors:Baba, S, Takeda, M, Okuma, J, Hirose, Y, Nishimura, A, Takata, M, Oda, K, Shibata, D, Kondo, Y, Kumasaka, T.
Deposit date:2019-05-28
Release date:2020-06-03
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.68000138 Å)
Cite:A hyperthermophilic cellobiohydrolase mined from a hot spring metagenomic data
To Be Published
4WZJ
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BU of 4wzj by Molmil
Spliceosomal U4 snRNP core domain
Descriptor: Small nuclear ribonucleoprotein E, Small nuclear ribonucleoprotein F, Small nuclear ribonucleoprotein G, ...
Authors:Leung, A.K.W, Nagai, K, Li, J.
Deposit date:2014-11-19
Release date:2015-01-14
Last modified:2024-01-10
Method:X-RAY DIFFRACTION (3.6 Å)
Cite:Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis.
Nature, 473, 2011

 

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