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- PDB-7umu: Structure of MAP kinase phosphatase 5 in complex with 3,3-dimethy... -

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基本情報

登録情報
データベース: PDB / ID: 7umu
タイトルStructure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1-((5,6-dihydrobenzo[h]quinazolin-2-yl)thio)butan-2-one, an allosteric inhibitor
要素Dual specificity protein phosphatase 10
キーワードHYDROLASE/INHIBITOR / phosphatase / protein-tyrosine phosphatase / dual specificity phosphatase / phosphatase-inhibitor complex / HYDROLASE-INHIBITOR complex
機能・相同性
機能・相同性情報


negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation / Signaling by MAPK mutants / negative regulation of oligodendrocyte differentiation / negative regulation of JUN kinase activity / RAF-independent MAPK1/3 activation / negative regulation of JNK cascade / JUN kinase binding / positive regulation of regulatory T cell differentiation / negative regulation of stress-activated MAPK cascade / myosin phosphatase activity / mitogen-activated protein kinase p38 binding / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / protein-serine/threonine phosphatase / oligodendrocyte differentiation / phosphatase activity / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / dephosphorylation / negative regulation of cell migration / protein-tyrosine-phosphatase / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / negative regulation of epithelial cell proliferation / response to lipopolysaccharide / nucleoplasm / nucleus / cytoplasm / cytosol
類似検索 - 分子機能
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
類似検索 - ドメイン・相同性
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-NUN / Dual specificity protein phosphatase 10
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.51 Å
データ登録者Gannam, Z.T.K. / Jamali, H. / Lolis, E. / Anderson, K.S. / Ellman, J.A. / Bennett, A.M.
資金援助 米国, 4件
組織認可番号
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR66003 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122473 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI055403 米国
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)MD122473 米国
引用ジャーナル: Eur.J.Med.Chem. / : 2022
タイトル: Defining the structure-activity relationship for a novel class of allosteric MKP5 inhibitors.
著者: Gannam, Z.T.K. / Jamali, H. / Kweon, O.S. / Herrington, J. / Shillingford, S.R. / Papini, C. / Gentzel, E. / Lolis, E. / Bennett, A.M. / Ellman, J.A. / Anderson, K.S.
履歴
登録2022年4月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年10月5日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Dual specificity protein phosphatase 10
B: Dual specificity protein phosphatase 10
C: Dual specificity protein phosphatase 10
D: Dual specificity protein phosphatase 10
E: Dual specificity protein phosphatase 10
F: Dual specificity protein phosphatase 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)107,33317
ポリマ-104,7006
非ポリマー2,63411
00
1
A: Dual specificity protein phosphatase 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,9153
ポリマ-17,4501
非ポリマー4652
0
タイプ名称対称操作
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,9153
ポリマ-17,4501
非ポリマー4652
0
タイプ名称対称操作
identity operation1_555x,y,z1
3
C: Dual specificity protein phosphatase 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,9153
ポリマ-17,4501
非ポリマー4652
0
タイプ名称対称操作
identity operation1_555x,y,z1
4
D: Dual specificity protein phosphatase 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,9153
ポリマ-17,4501
非ポリマー4652
0
タイプ名称対称操作
identity operation1_555x,y,z1
5
E: Dual specificity protein phosphatase 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,7602
ポリマ-17,4501
非ポリマー3101
0
タイプ名称対称操作
identity operation1_555x,y,z1
6
F: Dual specificity protein phosphatase 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)17,9153
ポリマ-17,4501
非ポリマー4652
0
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)65.650, 129.260, 82.840
Angle α, β, γ (deg.)90.000, 91.950, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and resid 321 through 465)
d_2ens_1(chain "B" and resid 321 through 465)
d_3ens_1(chain "C" and resid 321 through 465)
d_4ens_1(chain "D" and resid 321 through 465)
d_5ens_1(chain "E" and resid 321 through 465)
d_6ens_1(chain "F" and resid 321 through 465)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUGLYA3 - 147
d_21ens_1GLUGLYD2 - 146
d_31ens_1GLUGLYG2 - 146
d_41ens_1GLUGLYJ1 - 145
d_51ens_1GLUGLYM2 - 146
d_61ens_1GLUGLYO2 - 146

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要素

#1: タンパク質
Dual specificity protein phosphatase 10 / Mitogen-activated protein kinase phosphatase 5 / MKP-5


分子量: 17449.961 Da / 分子数: 6 / 断片: UNP residues 320-467 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DUSP10, MKP5 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: Q9Y6W6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: 化合物
ChemComp-NUN / 1-[(benzo[h]quinazolin-2-yl)sulfanyl]-3,3-dimethylbutan-2-one


分子量: 310.413 Da / 分子数: 6 / 由来タイプ: 合成 / : C18H18N2OS / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / L-DTT


分子量: 154.251 Da / 分子数: 5 / 由来タイプ: 合成 / : C4H10O2S2
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.36 Å3/Da / 溶媒含有率: 63.34 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 100 mM HEPES (pH 7.5) 200 mM ammonium acetate 25% (w/v) PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-E / 波長: 0.98 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2016年7月15日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.98 Å / 相対比: 1
反射解像度: 2.51→48.48 Å / Num. obs: 92335 / % possible obs: 99.77 % / 冗長度: 3.7 % / Biso Wilson estimate: 43.25 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.1324 / Rpim(I) all: 0.07974 / Net I/σ(I): 10.05
反射 シェル解像度: 2.51→2.6 Å / 冗長度: 3.7 % / Rmerge(I) obs: 1.111 / Mean I/σ(I) obs: 1.58 / Num. unique obs: 17403 / CC1/2: 0.512 / CC star: 0.823 / Rpim(I) all: 0.6661 / % possible all: 99.85

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータスケーリング
PHASER位相決定
Cootモデル構築
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 6MC1
解像度: 2.51→48.48 Å / SU ML: 0.3545 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 24.5755
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2284 3927 4.26 %
Rwork0.1973 88192 -
obs0.1986 92119 99.03 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 49.49 Å2
精密化ステップサイクル: LAST / 解像度: 2.51→48.48 Å
タンパク質核酸リガンド溶媒全体
原子数7143 0 172 0 7315
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00367478
X-RAY DIFFRACTIONf_angle_d0.648310111
X-RAY DIFFRACTIONf_chiral_restr0.04441090
X-RAY DIFFRACTIONf_plane_restr0.00471302
X-RAY DIFFRACTIONf_dihedral_angle_d19.44832784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.71880295007
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.697397605164
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.836423875311
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.795599158157
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.717221532052
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.540.34411330.32653141X-RAY DIFFRACTION98.53
2.54-2.570.36111400.32823081X-RAY DIFFRACTION98.68
2.57-2.610.33641420.3283198X-RAY DIFFRACTION98.55
2.61-2.640.36451480.33193126X-RAY DIFFRACTION98.5
2.64-2.680.35661370.30683137X-RAY DIFFRACTION98.82
2.68-2.720.35341310.30133143X-RAY DIFFRACTION98.91
2.72-2.760.29921590.28783124X-RAY DIFFRACTION98.77
2.76-2.810.25911430.2793138X-RAY DIFFRACTION98.68
2.81-2.860.31121200.26473181X-RAY DIFFRACTION99.07
2.86-2.910.29771710.26043111X-RAY DIFFRACTION99.18
2.91-2.960.28521270.26223200X-RAY DIFFRACTION99.11
2.96-3.020.31741280.25943095X-RAY DIFFRACTION99.11
3.02-3.090.31641540.2773176X-RAY DIFFRACTION99.17
3.09-3.160.2831320.27123166X-RAY DIFFRACTION99.13
3.16-3.240.26091370.24253147X-RAY DIFFRACTION99.12
3.24-3.330.23481420.21063167X-RAY DIFFRACTION99.19
3.33-3.430.27341330.21953145X-RAY DIFFRACTION99.24
3.43-3.540.24621340.19313165X-RAY DIFFRACTION99.52
3.54-3.660.24111370.18743172X-RAY DIFFRACTION98.95
3.66-3.810.22061470.1793151X-RAY DIFFRACTION99.25
3.81-3.980.19351440.15323131X-RAY DIFFRACTION99.27
3.98-4.190.19761410.1443149X-RAY DIFFRACTION98.92
4.19-4.460.19661460.14113153X-RAY DIFFRACTION98.71
4.46-4.80.14491410.12823138X-RAY DIFFRACTION98.79
4.8-5.280.16561370.14133164X-RAY DIFFRACTION99.28
5.28-6.050.20191390.16943179X-RAY DIFFRACTION99.49
6.05-7.610.20171460.17773163X-RAY DIFFRACTION99.55
7.62-48.480.11681380.12583151X-RAY DIFFRACTION99.28
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.399216881592.67743529757-4.633113084874.95453459323-5.137056434539.694492849030.4079565386150.3229673846190.397174705684-0.1511007742660.2307185971940.2950418064010.623786321799-0.98769367858-0.7512707049030.304157201336-0.0493091778015-0.06641887089440.450186017161-0.1034059667950.441566405456122.113994627-27.559203215898.5205137195
28.23262116001-1.07725272074-2.781769810927.676289432731.85958173372.532216762270.196704806572-0.846809059543-0.07608041522820.510772276561-0.1180670060350.673977081006-0.303986115582-0.8726928026430.07571202793990.279165163153-0.07491096391820.05883935274530.517565882482-0.01713954402110.441901326607123.827877621-25.3270180582105.963600462
39.15329232497-3.36789635211.949491453542.912488746851.543739377133.652210581180.144090446287-0.0988307920155-1.3807558640.938806763490.473011253941-0.411552716511.2655723238-0.995676571963-0.8727846250810.629881400061-0.08529652757610.1634018606520.400048932175-0.009069002232970.742261446703121.032530088-35.9432803536106.92542167
43.89907335842-0.3397570563680.7993513252790.9516596773491.667159675193.49892091515-0.0420307888885-0.139398163214-0.0599986666420.212973831196-0.06493457161420.4011504606990.140996380208-0.1520337920680.1990552031580.3309347748660.0266816026420.04412593708990.2333813577460.05001293704910.340387083168131.250360658-27.8457224042108.222493641
52.835890899122.689900733542.263480422213.176113517473.327456289175.286257076680.3462940984550.0531262316350.2077338924331.228120631060.1310036169210.4216349105540.760803621113-0.311126253036-0.3908562857140.4525235926940.0406541029443-0.01952544519990.3488292125310.06151235358420.384294373239134.040594207-33.4903382148110.88793819
65.0311831314-1.43917615617-0.08793849252842.71678656337-3.934823824577.270932320230.01619827915380.1188543338160.3279176467930.263861830149-0.152590374513-0.811534931341-0.7253810194570.1107231833090.02450018695680.2419198460960.00217547026042-0.02925023363140.227673234453-0.02596793900940.377355631045138.364551221-12.6731797283104.799955663
78.263249692814.700738621471.593155004433.305229481480.7111989247232.16633480591-0.2586029024830.548694352127-0.781020944681-0.2205215064430.668541559079-0.7374742494110.2930644360870.519932968191-0.3611963458430.3676529661020.06035371692120.08322723055940.408910603107-0.03233090624780.368421282115139.333730914-28.052851436296.4077843652
80.7173586723691.17252794569-0.5134260662422.79533769149-1.891150567682.47777696963-0.1375702328630.0796602765839-0.084827786589-0.192238306712-0.1093165965130.0270014371218-0.0142462565736-0.1498510606160.1488229490370.265186351930.02226753231230.006143784050.280792746152-0.03145764674110.382919096431131.082763006-22.364721510798.4731282452
93.98208177486-1.3019928395-1.182442471713.41238948673-1.271151934935.151699494110.2639258556150.192655343332-0.2755626282-0.610225843168-0.1554368159330.4177789268410.199421730971-0.169497729727-0.1542442872460.3621958061850.0270694095247-0.03537641977140.23121315826-0.04157032309810.311103685583126.548381843-17.269388037291.2051742195
108.93167722888-2.46605605557-5.623464561958.443855654585.664314787075.71591433540.2398342979550.1529852475310.341840765401-0.880956041938-0.0544960630713-0.535736505007-0.8562151005370.457299451468-0.1128889875470.3730849552850.028338852898-0.01508805041930.2608336843890.03464941883970.352687365303139.659990788-12.907703275889.5763803936
118.80875158186-1.84328732641-0.04886966062571.71728398172.048488683813.706612799920.401402511489-0.449305371768-1.0037355953-0.119668871059-0.3141427993340.2026802130590.397825686062-0.982394962086-0.1168896091630.794370236834-0.0488646849995-0.1216591695150.7146062553630.01006645111150.373089695763144.530033101-21.1992906136135.937908886
122.733991824441.776145005352.77561961979.699400168720.9014958159733.177572287650.423142393358-0.7465979795520.4836846207651.18443147829-0.1442596033370.268460050021-0.000554105256088-0.672216251402-0.1211088592250.5290465036370.09451426651560.08691815975780.45159093082-0.05122105706130.350585527396140.642307287-21.2123216571130.923065071
134.443748184681.010739527422.082989705223.13993447418-3.062031612375.255187424241.45730068248-0.479731542278-0.117085958520.266882646098-0.8417539671741.91492421951-1.72421163972-0.816995178347-0.4542928066810.931937514150.07006560432460.03582172402820.552405074794-0.1151758757090.69599497258134.736853044-13.3541240382133.589025938
144.630308839430.7939193338150.6129789816924.375041404331.302613606723.053541684460.440697830534-0.08121718934790.188647424817-0.140385721438-0.266162901314-0.302510152017-0.247063129225-0.125721036672-0.0219704531520.4636254013010.0675371885959-0.0159006907070.2770373985520.08454555280310.319714190411139.289920533-19.5036371283123.106364855
157.12749893938-4.22473391423-0.3704831470597.334115466661.223744092434.769942772730.05988359871450.2851484739560.132495335811-0.205492405584-0.5313327919340.425426303346-0.188447168231-0.02917355760190.4220920941690.394120443593-0.0260310806538-0.02184560579340.2296800339770.03830462809210.222271237511142.331428515-22.8458057069118.55843099
168.34851643735-3.51239576041-1.908398872273.951640529315.156029205738.520914433060.04188421443460.0452302174421.23708062709-1.1618796382-0.528581629176-1.04023128082-1.43377218441.292280230860.3123112371240.717735552884-0.0844603972367-0.05654968396280.5583460276170.3004183434250.352043950745153.342718347-17.0781651796120.856299035
175.91384823236-1.644436568043.146918620650.9028213425260.1167762255114.07818313016-0.111636669873-0.06393268296750.5444383729810.167802383921-0.0988438532522-0.357716942791-0.6075626619740.2011955888580.1632193329310.499896903545-0.03325782782450.05698755423650.3102850980260.09156859117570.33600611425149.897995586-22.5058781119127.266657695
187.41513824013-2.57001891363-3.733231416135.572763835011.208982347192.39537094451-0.847903098323-0.745927216240.3160214259620.2098708895390.316651142405-0.590648287560.3352379540940.5559710245240.3539787715030.559039468805-0.0340051830064-0.1837045564820.4377080176410.02676066887770.381904764727157.416267261-27.5192188262135.245905364
197.88640024559-1.31862099272-3.428695518088.104045513717.366020734147.37550318792-0.363149223928-0.0311635633449-0.0813577829819-0.15656351638-0.0799315267435-0.599593264492-0.0809279488704-0.05469318316970.2039284871870.4160686887920.02025923451160.03218625522410.3176485233380.1476764337290.268266922339146.657067371-33.5577291176132.45776439
206.510983781635.295687768744.470907331254.452521785934.099518005766.8590649016-0.6238101490550.805359076807-0.509046160326-0.2554077733250.496979318408-1.0771603394-0.3236736420961.131232298690.1889985868240.4494948284450.0706634298632-0.01124561007020.5355272614960.07628994196110.514844681646161.79822882-31.3495677441123.035760476
214.801883308370.2361857023980.02792922681549.35208724565-0.705570760788.490627715770.0343106169838-0.1570582279770.530893709395-0.0638495441129-0.1619895360951.02913571876-0.0718349038287-0.8238782647860.2386687074580.303638363898-0.05539301592550.03943927598560.326784925919-0.08246724465710.494590660147119.415734857-49.138617456185.6343480146
222.2878193003-1.70031264911-1.89572993064.535254585060.5607490447371.474716066930.1263223385530.2740277864850.0856283000235-0.095585518666-0.09050660861020.0468081730887-0.18792596559-0.0867705505941-0.02715430899630.366673326778-0.0678280084861-0.02150353886720.328399537474-0.04723516836080.259758978512131.546190097-47.343626474582.7822491783
233.83216447303-4.44823917306-5.717549450028.493055250825.881015943828.854176440710.109957425356-0.886345453887-0.1230432726761.58176099290.227053451651-0.7832179668350.2418869553090.47739288421-0.3978380683940.661323141978-0.105453325121-0.1343132354610.4522649826410.01472653805650.448837024167134.407640195-56.127102153992.1106205954
240.905482071822-0.0148567636817-0.665674441516.200017923061.898938144351.345121901350.119244459356-0.194404799245-0.04185180532130.678921747818-0.0622428993798-0.1838526238070.260046392068-0.01577103765260.03638210507130.422338543462-0.0379986330086-0.08799565097450.331845330127-0.04749797677810.335180794513127.778419479-57.628834159985.3493666473
255.55420343761-0.723598029402-2.287277668337.91069555994-3.206975766494.972146766480.258364500308-0.141242033563-0.3874589151280.0544426304288-0.1155058071761.125440081380.53051880046-0.0302260770726-0.05343814310670.510468445799-0.135359352044-0.1045904528940.358397262532-0.06203273782840.413370735507122.307297214-65.608648641381.8179609085
264.653635132310.545645081750.1398522165554.32766869779-4.346339836524.629294730350.1425355327430.137776791889-1.24485502530.421421755237-0.469391224305-0.4775690046520.9895723310940.4839282675250.5351674958160.580014868237-0.0314301523387-0.04139063996720.402900260987-0.1082121470020.574677874328135.858331663-70.051116331582.5118999904
277.92285468546-4.26390372659-0.7673807722593.698241737091.105742196290.42436208421-0.617387083255-0.801520598188-0.01823972573770.1189925941250.211931056478-0.4689843195110.2997349495270.1711675620670.4448432165740.2991637282660.0861021498765-0.05124133050.513198572457-0.1017873594310.575441745095172.011055071-18.3280589251103.614556771
286.19656846878-2.624929193940.2426969640055.557490371361.650255410636.09958896714-0.341816759425-0.42804123701-0.3976621049750.536679710560.378667535294-0.1836645091540.5359718416570.200320088739-0.09582465257820.331730009469-0.05826344595620.001998031388180.439913057165-0.0485760532250.578485193988168.085744183-10.9875412541110.701328835
295.50951090688-0.8912449408863.593615529212.510129768151.708719247157.418135053090.112179161576-0.3209137262990.2096539464180.2010053450910.0870691053161-0.3410453775510.0820823444316-0.0766986925686-0.3889504766360.287956986022-0.0235433894928-0.008662650163020.373334156392-0.05710353395630.60569077396162.730264191-5.53837168694103.67076067
306.84085083465-3.957010332194.481554589893.70875892373-1.624186190753.341527827240.01924394254220.4717870215751.6336608394-0.278768769051-0.0832094024709-0.629215071491-0.06893778382990.5827653148170.04358989213650.363043794377-0.03703318756290.06426656501480.46333661422-0.007391933988020.605744175216171.436241336-6.0224631085494.4680670934
312.793597899060.6638129115791.105307380925.519812691043.453801135135.57332256033-0.02299638637620.2232874795630.101022076692-0.02324079952770.0468245456708-0.06054186696480.1404364809340.108699206159-0.04002376746690.252619735632-0.01847272154850.02795118899410.3554263193180.02576890657940.427252242548167.334161236-18.159563145596.0626815767
327.333389964284.61187077943-5.34383291237.55697088039-3.808943065738.79315646964-0.4463859183570.709691404930.0326908750578-0.988099830330.1682314076-0.005025859771660.366261729613-0.1261688762620.1786940341190.322909033905-0.02295288419580.00227580297470.4256582284570.01411846666540.437035993963162.05677231-14.310016706584.0721097556
336.915710117841.49754574159-1.992143052957.98105547636-1.32121510942.748744630980.01620709425320.009812734603490.833458587512-0.2472365117570.5624201065710.573894763144-0.771185925298-0.15121032381-0.6145012177110.4868827594940.0002940787549710.0274870932140.4756124396940.06673394512540.34211197247144.940239218-29.75643965968.5627920083
342.69445895696-2.03796812671-2.402515144163.500520344811.330756005772.263502089690.387797750998-0.5210395729810.0509003776701-0.1401005008120.423959064590.502937756542-1.53427286493-0.248505422657-0.6366049686750.7184478239350.0313276352634-0.03504215051160.615172179898-0.03845874933430.334924713285139.430282667-32.575747613860.1949221316
356.877928538742.07699465029-3.879648900532.29446124901-2.416666732296.124977764990.527455606595-0.05652952900440.201996813428-0.055977533102-0.02265529048080.255297890437-0.352835042026-0.215751939025-0.4224942450280.3551701153930.038832895143-0.0067500659970.224433996151-0.02304953087780.295189360191140.715823369-38.402335352171.5180394208
365.437821561190.04764220493644.100429560993.012579499942.43907050657.921442074930.0407256520755-0.2100197663180.30436113490.206451549157-0.1904647160770.03622008899310.494372872966-0.5978789264270.08504098366430.377892649354-0.05732163622390.07764624238280.218737656445-0.007839054375230.275011151343142.34949801-40.661124673777.2528133209
370.774816313236-0.3280576592341.145421473034.784768329740.9599933508732.091525794060.1734847860760.337614922183-0.250848568432-0.353342599138-0.125751552742-0.5194607678250.6999501419860.8016031220460.08440646551680.4080606300160.05442574539990.01251663939870.47872070944-0.01027358649130.479092251385154.406513917-42.750629173.987637954
387.05695098308-1.37077281531-3.039957487942.25214262863-1.095160332126.03436994046-0.4076336188180.2237489129620.09408412344670.0013817375453-0.1367629737-0.07739305959050.404841464220.1200059943490.6478198933330.413620785316-0.0214042931228-0.01298142937150.2232585214830.02804480827290.282644753926145.848363639-34.74889996371.0211469461
394.854254025264.007374211541.741344551754.380956432440.6315829150895.807594689970.02103024586460.5026632287910.367472793244-0.4420819007130.145941163383-0.177289621581-0.3958055920640.585531043441-0.1867850930050.3913011545430.006308863116740.05595969714580.3168553352380.01557041096710.3412661862155.917943299-28.642259864276.9353104169
407.55428227464-2.31038688577-4.614985777427.427955643071.573411377943.05023866007-0.298855829643-0.2355110571980.006821642156690.450883080870.582317354525-1.32991347859-0.05658884742330.977494927996-0.2339343529180.3864087746820.0416661362017-0.02027947813060.451582143288-0.07133449024970.388052884867161.153149374-34.818673512386.1734383366
411.470335984012.41597924824-2.266455351338.33426404032-2.916424854123.61799108224-0.114655536464-0.213282247703-0.01490838116450.774422125584-0.03618948131280.5397282467560.0130612199202-0.5926484481840.09111070289390.499943107257-0.03233644127490.2466681305090.61132738865-0.1469218137080.69634429616144.11635428911.8154883594119.381948592
429.20072744127-4.51409414137-0.3835553073744.489236030372.576378996022.728137813880.152117894128-0.2596457289180.3420310880891.87083056813-0.663472384649-0.1573530118550.760816336065-0.03716697971180.2745553769110.550706063625-0.1335914593640.04604092364690.531051231298-0.08556777220710.404715641203150.5385385944.88007199137119.869831413
438.18571398506-1.499115082541.68769121526.553784981651.064974672994.48981936140.0722582934934-0.730173873291-0.2941585507780.685311398722-0.1286147804130.7333539798430.302346178625-0.6904339035740.04913042744930.377711414594-0.0874095083270.0167954266690.426546506767-0.1121710884020.423639999913148.5063077871.29715264641114.676061709
444.405472646423.91375880411-4.166170289373.8468520088-2.528689209737.559665402290.1712247036080.03077775809310.3078048099070.41253487914-0.1257572137110.23198316710.3554851188350.110390457597-0.2779827194330.269241488532-0.0547662459939-0.009929570106990.43113804174-0.1486713691710.460229048077148.122734374-2.90507879786108.759270045
453.627411373942.952817626581.965511042979.27569990606-4.687665263157.3471812619-0.47573064774-0.218350083746-0.167206154911-0.688846284494-0.406769254594-0.6255982200370.257813182190.01900230046820.7367691419560.379354147094-0.1323061012210.07766243759050.6144133183-0.2104366777630.437723752805164.57953969811.969462859108.654607929
465.616306409376.09956366792-4.286866471639.12732109146-2.610619468146.07792375251-0.3414568170961.854497300390.794755868299-0.8622342222570.7434147796811.09912191538-0.480685597473-0.374997556559-0.3594192322720.505318169771-0.0679820153639-0.05823731312060.569100604236-0.0590841558760.40840343994147.975930712.5709882354103.561127567
473.420056759212.38907480491-0.733319512697.49391264267-1.22285952692.24618392364-0.134302127650.267805948127-0.045123109783-0.146347277580.1393471186770.275853104226-0.2766894006370.0483635271393-0.03521920387740.295583350421-0.0855286875260.01702834367490.434514770561-0.1280818216860.315410886714151.06982093513.8941374126112.593673032
486.94023194841-1.63488476984-1.197310584688.308271902410.1386078402871.617473964090.154103266614-0.2904031866340.7679890015750.543618337469-0.3015320334960.30298934836-0.185711552049-0.1543016674220.09806446067680.404412025301-0.08397560348180.03612348658330.532824423375-0.2065249559320.375291818387152.74891517221.7712407162119.070238643
498.5434129907-6.471461108997.134811357765.50012592509-5.556091976956.03247233661-0.2618897600531.068798792520.917682695805-0.621996691203-0.382163557144-0.380974701689-0.8463588367931.051912304940.5678716843930.61935420225-0.1759388314650.06956976002390.560574255483-0.04031697955630.412545186761158.15666840125.5914984633106.385357681
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 319 through 328 )AA319 - 3281 - 10
22chain 'A' and (resid 329 through 339 )AA329 - 33911 - 21
33chain 'A' and (resid 340 through 345 )AA340 - 34522 - 27
44chain 'A' and (resid 346 through 362 )AA346 - 36228 - 44
55chain 'A' and (resid 363 through 372 )AA363 - 37245 - 54
66chain 'A' and (resid 373 through 383 )AA373 - 38355 - 65
77chain 'A' and (resid 384 through 400 )AA384 - 40066 - 82
88chain 'A' and (resid 401 through 425 )AA401 - 42583 - 107
99chain 'A' and (resid 426 through 448 )AA426 - 448108 - 130
1010chain 'A' and (resid 449 through 467 )AA449 - 467131 - 149
1111chain 'B' and (resid 320 through 326 )BD320 - 3261 - 7
1212chain 'B' and (resid 327 through 339 )BD327 - 3398 - 20
1313chain 'B' and (resid 340 through 345 )BD340 - 34521 - 26
1414chain 'B' and (resid 346 through 362 )BD346 - 36227 - 43
1515chain 'B' and (resid 363 through 383 )BD363 - 38344 - 64
1616chain 'B' and (resid 384 through 399 )BD384 - 39965 - 80
1717chain 'B' and (resid 400 through 427 )BD400 - 42781 - 108
1818chain 'B' and (resid 428 through 441 )BD428 - 441109 - 122
1919chain 'B' and (resid 442 through 448 )BD442 - 448123 - 129
2020chain 'B' and (resid 449 through 465 )BD449 - 465130 - 146
2121chain 'C' and (resid 320 through 345 )CG320 - 3451 - 26
2222chain 'C' and (resid 346 through 383 )CG346 - 38327 - 64
2323chain 'C' and (resid 384 through 400 )CG384 - 40065 - 81
2424chain 'C' and (resid 401 through 427 )CG401 - 42782 - 108
2525chain 'C' and (resid 428 through 448 )CG428 - 448109 - 129
2626chain 'C' and (resid 449 through 466 )CG449 - 466130 - 147
2727chain 'D' and (resid 321 through 333 )DJ321 - 3331 - 13
2828chain 'D' and (resid 334 through 362 )DJ334 - 36214 - 42
2929chain 'D' and (resid 363 through 383 )DJ363 - 38343 - 63
3030chain 'D' and (resid 384 through 399 )DJ384 - 39964 - 79
3131chain 'D' and (resid 400 through 448 )DJ400 - 44880 - 128
3232chain 'D' and (resid 449 through 465 )DJ449 - 465129 - 145
3333chain 'E' and (resid 320 through 339 )EM320 - 3391 - 20
3434chain 'E' and (resid 340 through 345 )EM340 - 34521 - 26
3535chain 'E' and (resid 346 through 362 )EM346 - 36227 - 43
3636chain 'E' and (resid 363 through 383 )EM363 - 38344 - 64
3737chain 'E' and (resid 384 through 399 )EM384 - 39965 - 80
3838chain 'E' and (resid 400 through 412 )EM400 - 41281 - 93
3939chain 'E' and (resid 413 through 448 )EM413 - 44894 - 129
4040chain 'E' and (resid 449 through 466 )EM449 - 466130 - 147
4141chain 'F' and (resid 320 through 328 )FO320 - 3281 - 9
4242chain 'F' and (resid 329 through 339 )FO329 - 33910 - 20
4343chain 'F' and (resid 340 through 362 )FO340 - 36221 - 43
4444chain 'F' and (resid 363 through 372 )FO363 - 37244 - 53
4545chain 'F' and (resid 373 through 383 )FO373 - 38354 - 64
4646chain 'F' and (resid 384 through 400 )FO384 - 40065 - 81
4747chain 'F' and (resid 401 through 427 )FO401 - 42782 - 108
4848chain 'F' and (resid 428 through 448 )FO428 - 448109 - 129
4949chain 'F' and (resid 449 through 467 )FO449 - 467130 - 148

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月:コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか? / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例:em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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