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- PDB-9na5: IRAK4 in Complex with Compound 24 -

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基本情報

登録情報
データベース: PDB / ID: 9na5
タイトルIRAK4 in Complex with Compound 24
要素Interleukin-1 receptor-associated kinase 4
キーワードIMMUNE SYSTEM / TRANSFERASE/INHIBITOR / Kinase / Phosphorylated / Signaling Protein / Inhibitor Complex / TRANSFERASE-INHIBITOR complex
機能・相同性
機能・相同性情報


IRAK4 deficiency (TLR5) / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / neutrophil mediated immunity / interleukin-1 receptor binding ...IRAK4 deficiency (TLR5) / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / neutrophil mediated immunity / interleukin-1 receptor binding / interleukin-1-mediated signaling pathway / extrinsic component of plasma membrane / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / JNK cascade / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of smooth muscle cell proliferation / cytokine-mediated signaling pathway / Interleukin-1 signaling / kinase activity / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of canonical NF-kappaB signal transduction / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / endosome membrane / intracellular signal transduction / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / cell surface / magnesium ion binding / extracellular space / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
: / Interleukin-1 receptor-associated kinase 4
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: 1.73 Å
データ登録者Ferrao, R. / Lansdon, E.B.
資金援助1件
組織認可番号国
Not funded
引用
ジャーナル: J.Med.Chem. / 年: 2025
タイトル: Discovery of Edecesertib (GS-5718): A Potent, Selective Inhibitor of IRAK4.
著者: Ammann, S.E. / Cottell, J.J. / Wright, N.E. / Warr, M.R. / Snyder, C.A. / Bacon, E.M. / Brizgys, G. / Chin, E. / Chou, C. / Conway, A. / Dick, R.A. / Ferrao, R.D. / Garrison, K.L. / Hammond, ...著者: Ammann, S.E. / Cottell, J.J. / Wright, N.E. / Warr, M.R. / Snyder, C.A. / Bacon, E.M. / Brizgys, G. / Chin, E. / Chou, C. / Conway, A. / Dick, R.A. / Ferrao, R.D. / Garrison, K.L. / Hammond, A. / Lansdon, E.B. / Link, J.O. / Mukherjee, P.K. / Murray, B.P. / Mwangi, J. / Ndukwe, M.S. / Park, G.Y. / Serone, A.P. / Suekawa-Pirrone, K. / Yang, Z.Y. / Zipfel, S.M. / Taylor, J.G.
#1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019
タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
履歴
登録2025年2月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年5月28日Provider: repository / タイプ: Initial release
改定 1.12025年6月18日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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: Interleukin-1 receptor-associated kinase 4
B: Interleukin-1 receptor-associated kinase 4
C: Interleukin-1 receptor-associated kinase 4
D: Interleukin-1 receptor-associated kinase 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)140,24119
ポリマ－136,8624
非ポリマー3,37915
水15,709872
1
A: Interleukin-1 receptor-associated kinase 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)34,9884
ポリマ－34,2161
非ポリマー7733
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Interleukin-1 receptor-associated kinase 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,0845
ポリマ－34,2161
非ポリマー8694
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Interleukin-1 receptor-associated kinase 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)34,9884
ポリマ－34,2161
非ポリマー7733
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Interleukin-1 receptor-associated kinase 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,1806
ポリマ－34,2161
非ポリマー9655
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)87.261, 141.638, 111.259
Angle α, β, γ (deg.)90.000, 93.560, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDモデル要素
11A-767-

HOH

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要素

#1: タンパク質
Interleukin-1 receptor-associated kinase 4 / IRAK-4 / Renal carcinoma antigen NY-REN-64


分子量: 34215.516 Da / 分子数: 4 / 断片: kinase domain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IRAK4
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase
#2: 化合物
ChemComp-A1BWY / (6P)-6-[(8R)-3-cyanopyrrolo[1,2-b]pyridazin-7-yl]-4-({(1s,4S)-4-[1-(difluoromethyl)-1H-pyrazol-4-yl]cyclohexyl}amino)-N-[(2S)-2-fluoro-3-hydroxy-3-methylbutyl]pyridine-3-carboxamide


分子量: 580.604 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C29H31F3N8O2 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 11 / 由来タイプ: 合成 / 式: SO4
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 872 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY
Has protein modificationY

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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: 2.51 Å3/Da / 溶媒含有率: 50.94 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 2.15 M ammonium sulfate, 100 mM Hepes-NaOH at pH 7.0

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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: ALS / ビームライン: 5.0.2 / 波長: 0.99999 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年5月3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: 0.99999 Å / 相対比: 1
反射解像度: 1.73→48.5 Å / Num. obs: 139999 / % possible obs: 99.3 % / 冗長度: 3.4 % / Biso Wilson estimate: 25.95 Å2 / CC1/2: 1 / Net I/σ(I): 12.09
反射 シェル解像度: 1.73→1.79 Å / Num. unique obs: 13919 / CC1/2: 0.51

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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データ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 1.73→48.5 Å / SU ML: 0.233 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 25.6462
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2274 7037 5.06 %
Rwork0.1882 132026 -
obs0.1902 139063 99.29 %
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: 40.17 Å2
精密化ステップサイクル: LAST / 解像度: 1.73→48.5 Å
タンパク質核酸リガンド溶媒全体
原子数9056 0 223 872 10151
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00739473
X-RAY DIFFRACTIONf_angle_d0.910812832
X-RAY DIFFRACTIONf_chiral_restr0.05931425
X-RAY DIFFRACTIONf_plane_restr0.00811622
X-RAY DIFFRACTIONf_dihedral_angle_d10.21041285
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.3392150.31924426X-RAY DIFFRACTION99.87
1.75-1.770.33832560.30164391X-RAY DIFFRACTION99.87
1.77-1.790.3552610.30394370X-RAY DIFFRACTION99.83
1.79-1.810.3372470.29224430X-RAY DIFFRACTION99.66
1.81-1.840.32262390.28554392X-RAY DIFFRACTION99.89
1.84-1.860.34732230.28794431X-RAY DIFFRACTION99.76
1.86-1.890.32912410.28184386X-RAY DIFFRACTION99.48
1.89-1.920.3622340.32134302X-RAY DIFFRACTION97.72
1.92-1.950.3142540.30534232X-RAY DIFFRACTION96.83
1.95-1.980.25892680.2264419X-RAY DIFFRACTION99.85
1.98-2.010.25312420.19744408X-RAY DIFFRACTION100
2.01-2.050.22692420.19744443X-RAY DIFFRACTION100
2.05-2.090.27222440.22674356X-RAY DIFFRACTION99.29
2.09-2.130.25542520.20384391X-RAY DIFFRACTION99.66
2.13-2.180.26362260.19094428X-RAY DIFFRACTION99.76
2.18-2.230.24782080.20144413X-RAY DIFFRACTION99.46
2.23-2.290.33242230.26634217X-RAY DIFFRACTION94.69
2.29-2.350.23042260.19284433X-RAY DIFFRACTION99.76
2.35-2.420.24692210.18054456X-RAY DIFFRACTION99.98
2.42-2.50.22272260.18314409X-RAY DIFFRACTION99.85
2.5-2.580.24112350.18134434X-RAY DIFFRACTION99.89
2.58-2.690.23562390.18194395X-RAY DIFFRACTION99.48
2.69-2.810.24082380.18694433X-RAY DIFFRACTION99.59
2.81-2.960.21782170.17764414X-RAY DIFFRACTION99.55
2.96-3.140.21662190.16774438X-RAY DIFFRACTION99.57
3.14-3.390.19312590.16294433X-RAY DIFFRACTION99.58
3.39-3.730.18712430.15154370X-RAY DIFFRACTION98.95
3.73-4.270.1692150.1434404X-RAY DIFFRACTION98.32
4.27-5.370.18812140.15294448X-RAY DIFFRACTION99.34
5.37-48.50.1942100.19314524X-RAY DIFFRACTION99.25
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.992121772620.661907527172-4.100102034042.298009968120.2881514306553.695824973960.03634951056350.4722451077690.333369409457-0.1212703928980.08729670425980.0796732674387-0.126750159153-0.17741699528-0.1194952419260.1782281347720.0111841470665-0.03058524208950.1715342484030.006396232473040.1655228081137.635343056949.861877138516.56383005667
24.469088835362.245144378310.5392808924918.81405546347-0.6121719304053.88951446543-0.04106180201460.2550243387910.407484306152-0.4350972380780.0933302925283-0.373645235821-0.4487979711670.124016044763-0.05469622070210.202169290521-0.002692949143110.06499100413660.1855639070690.01925233026040.16541066472310.26973776410.957956248910.0001628502
35.96914490558-5.665215604244.062456951699.32312767896-3.895007089062.00594628187-0.3051751259650.08202895408611.089036216040.606714410189-0.340938511505-1.09083363044-1.346659626180.5586686207780.6457517512570.449125521942-0.117581370854-0.01402996002910.378112620592-0.0498609504090.4480999073923.22521535518.542538612113.6536161311
44.909542452932.0001185507-3.719169780692.05511973917-1.789621074242.00359561699-0.1222541767240.24060109630.184688390852-0.1377223343240.085983265838-0.112962671545-0.09511216818690.07585968851090.0338736846890.249745612151-0.0132386886558-0.005592934417650.186078671793-0.02890955270490.33113786911718.79979945399.8848506468314.6107890375
53.074505018-0.189166251826-1.403129077231.449520532041.028978891512.48759915867-0.0258423579007-0.129770352647-0.1236951359240.20755951583-0.032781038628-0.1207371677030.163906295779-0.03351941316070.05604053475590.232575175984-0.00019805122863-0.01522485795140.127887353881-0.004298368794970.1982371003546.862967032410.536429692428.3117064884
67.271532305193.6840629828-1.151104236795.21311167374-1.042089598213.38611027383-0.06865963373560.0178373247984-0.0762876044932-0.1013359991440.158466628999-0.487844122475-0.04778469900860.271928824241-0.08308544788390.1653258833690.01564657625020.01912032499790.174176166624-0.05339090056160.17546236623414.087127318114.494562077825.5168079098
74.83382246761.127507402521.538369521716.96293843347-0.246272685815.937523871550.01968162055780.1080024804980.791152031389-0.06487642387350.186615046022-1.09909851763-0.2361096258441.12425628102-0.2075352123780.299960543609-0.0558033979530.03029072838360.385262386106-0.1326158551120.56273792201219.98407376131.016602568426.0524104685
83.7939160776-0.0257908541508-1.11153952655.15318111065-0.1639249244264.01851976766-0.00471879058243-0.1204561741190.473441466798-0.002879725181940.08872389739010.221697541518-0.22405763356-0.178103050201-0.07904463058870.195965218372-0.01915503061010.003208297449660.135455781287-0.05360013689230.2263214915644.3113535242325.254372612231.82422967
92.003648015730.110307368626-4.464053623793.42247094380.1649256280662.002334878620.435205464915-1.483717261.485119927421.69509493912-0.4000473514550.787077952962-1.168562640180.0566679414638-0.01876257051220.762805689787-0.08709667010150.07903507083260.625303231116-0.1785295781250.663607191854-0.58329405293230.038506159142.214111679
105.195023992063.881237945033.078587023333.007685164411.68792604335.414861473680.36343710213-1.022673753420.469373698240.659249525044-0.44171630080.387288350860.0531260491293-0.6181219341120.09324088482310.3236169015160.01072328454850.05803637573360.326100175758-0.07768588690680.2644004403280.62946312186317.800629350442.5132715713
116.215606809331.488359771990.613662398012.00150761908-1.083037516363.796083366820.276666004261-0.7995684346750.1009841682911.41534186375-0.126116795195-0.853781581314-0.1892208518170.228391037436-0.1603974649340.424142174853-0.0455483210925-0.08939151048710.429326283877-0.1349621312620.29226145451416.096513303420.586056741842.1959182482
122.65202053541-0.221594499121-0.6977458025192.71269090835-0.7095841310012.73843932069-0.00561186863838-0.4587234651480.1011058935850.683299427710.1221646825220.342543172866-0.184142699531-0.290635209852-0.08999854128230.3483943573120.01479238517360.07943221882490.2580442526990.001497915910740.285411898644-32.280378315213.533401040338.2052371014
134.7322698479-2.55815185496-0.8297360622743.570060666730.7220349086062.342437418730.2419613050570.3676185027780.580818546047-0.432761556689-0.115167971866-0.178746938427-0.312698801505-0.0605421597455-0.1235085343590.2677816023430.02040866714960.06701636090310.1913850499550.07558627046270.274592899689-24.849205740224.905065868219.5657361575
143.336013382361.739839328392.610401438174.73714913417-2.196895334136.761318432110.04145847112980.9122320250140.1242180827490.03168233761220.05808015743230.0924704302101-0.0161246487974-0.340978170976-0.09443860379420.194837347488-0.0199434774513-0.0007039613757920.180262610788-0.0199157636620.162419572948-15.2552247135-4.29677320394.29771415597
159.021030023010.1539112112790.7926141210273.20090980721-0.1548269787145.612535059660.07005932908160.0840448098226-0.610155198239-0.06923002307360.0581139098361-0.7900112436650.6397242530680.11768952378-0.1279183486750.212840797123-0.0189799628709-0.0155246431030.17294003791-0.03352656704140.20027578308-6.91684567504-7.9613079095210.4414118354
164.901855793860.176229220556-1.075608239638.471281812290.6037972235243.85045123902-0.03902900376630.0420146198847-0.842492972209-0.221091536464-0.07658668014430.4943619923120.757153210394-0.4109452289670.1232991569070.263688362232-0.0408572951344-0.0697265063170.245896188690.01598996196420.218119681359-21.768732735-12.815340351911.5132863752
174.51593324931-0.2580832558120.3616274393331.868415159550.2507317815246.42681458305-0.09841895080380.362021182829-0.185708796931-0.179730422781-0.08160339451660.223787728250.209247903949-0.5964313311860.1850579750740.17444809234-0.0517309140225-0.005282144382330.1668481670580.009766930194290.271127190838-22.1375718317-6.8366128327214.3098863935
183.13604767908-0.2758644208841.004433462581.5524658878-0.7744101893592.29384552428-0.0363166844964-0.1692057488880.1058000914520.20545595554-0.01297843655070.0731777786132-0.1247123986090.01659841066290.04422119085210.207032680448-0.00806149673470.002678687898540.115133540555-0.004813052180080.183334953272-10.1532127719-7.8222773541927.6863048584
196.810899606241.171208253240.06823424911624.531916720481.515036290894.03960064052-0.246460273951-0.0879546051523-0.147927224614-0.08050774370590.2066751193090.387053051229-0.00838206781832-0.2748079935930.04243275477190.1299727680820.0264286777758-0.01469206659520.1655513186660.05309496491590.132338345564-16.6182407604-11.582864117625.7493413029
208.258694528273.68802422541.184790901975.393560219952.135059238113.79257972063-0.0102587007018-0.0851997165414-0.6251726791570.02398792593710.05685808910310.6690752303320.718370481344-0.601364241765-0.02840996790490.387311372213-0.0891392961807-0.06001859673440.3658037505210.06604793951980.327410725721-24.3496935822-22.455308734122.1462679139
215.426776667671.121234535781.080406091794.981576688480.9754270339233.94898817804-0.00120958823699-0.0550791504478-0.5376207747620.009120895410480.02128948037620.03564489604030.266640448014-0.0640215233235-0.001327080910170.196173272455-0.01666446874780.004485678850060.1451231273520.07450992580730.218343561585-11.3405305891-24.558075763129.7645827326
229.88799938831.919187335664.793116622385.64672142057-0.6728372838932.00146705450.645061607246-1.39123561924-1.605149082161.52131520693-0.457626306621-0.9335107801871.261454813720.143497177934-0.181773729370.615182815994-0.0505785273792-0.1138004180090.5332878808420.2063499810090.666739926759-2.21110066332-27.204111099141.0334160522
239.885592667823.0717142282-2.417346008841.38686024329-0.1599029608775.920841926830.521976130505-1.5275656387-0.4198573265550.703657321929-0.422189887355-0.199927458873-0.2012374162630.531398379063-0.09899375066370.342789090904-0.00602718836554-0.03718987878930.3275412508230.07406123667730.239594901178-4.36478134507-14.855625128341.9963853963
247.24910583122.168225871710.2793266336849.846538297311.377013686213.757336354740.285662900539-0.7434338110930.1117773281991.35110298337-0.2539768507240.7980584928310.292409051528-0.665942415279-0.03362718326780.381956491898-0.03310027182270.1155804254820.4304176913390.09683957690770.209882488937-19.4837760415-18.018030552441.4101740916
253.90419298415-0.338661109887-0.07577773715563.777280283850.7848954430336.48956343969-0.0976660776002-0.695187661145-0.2250612578730.8151196615280.109305619847-0.04227952357110.5997367042470.433727472489-0.01409553307530.4980703028020.0281470012456-0.07634088296370.364690378179-0.05266079337560.28193795630129.0964136415-8.6326533838944.9630696142
264.26996355424-1.716984339390.3091890445653.688286283740.1421503802442.10856937440.09482018835660.0821502589197-0.346521656433-0.110201842383-0.00869113361297-0.07626683866580.2451974314880.197183467961-0.09244132651290.1832563500090.00165995294864-0.02916488792090.166758890796-0.02134534388840.17991705998824.1160135611-18.64288799822.8095215193
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 164 through 197 )AA164 - 1973 - 36
22chain 'A' and (resid 198 through 222 )AA198 - 22237 - 59
33chain 'A' and (resid 223 through 239 )AA223 - 23960 - 76
44chain 'A' and (resid 240 through 258 )AA240 - 25877 - 95
55chain 'A' and (resid 259 through 304 )AA259 - 30496 - 141
66chain 'A' and (resid 305 through 332 )AA305 - 332142 - 169
77chain 'A' and (resid 333 through 365 )AA333 - 365170 - 198
88chain 'A' and (resid 366 through 395 )AA366 - 395199 - 228
99chain 'A' and (resid 396 through 412 )AA396 - 412229 - 245
1010chain 'A' and (resid 413 through 436 )AA413 - 436246 - 269
1111chain 'A' and (resid 437 through 458 )AA437 - 458270 - 291
1212chain 'B' and (resid 165 through 349 )BC165 - 3491 - 175
1313chain 'B' and (resid 350 through 458 )BC350 - 458176 - 284
1414chain 'C' and (resid 162 through 184 )CG162 - 1842 - 24
1515chain 'C' and (resid 185 through 205 )CG185 - 20525 - 45
1616chain 'C' and (resid 206 through 239 )CG206 - 23946 - 77
1717chain 'C' and (resid 240 through 258 )CG240 - 25878 - 96
1818chain 'C' and (resid 259 through 304 )CG259 - 30497 - 142
1919chain 'C' and (resid 305 through 324 )CG305 - 324143 - 162
2020chain 'C' and (resid 325 through 350 )CG325 - 350163 - 183
2121chain 'C' and (resid 351 through 395 )CG351 - 395184 - 228
2222chain 'C' and (resid 396 through 413 )CG396 - 413229 - 246
2323chain 'C' and (resid 414 through 436 )CG414 - 436247 - 269
2424chain 'C' and (resid 437 through 458 )CG437 - 458270 - 291
2525chain 'D' and (resid 164 through 269 )DK164 - 2691 - 100
2626chain 'D' and (resid 270 through 458 )DK270 - 458101 - 285

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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://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

他の情報も見る