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- PDB-7un0: 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: 7un0
タイトルStructure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1-((9-chloro-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 (ホスファターゼ) / protein-tyrosine phosphatase / ddual 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 / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / 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 / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / 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 / positive regulation of regulatory T cell differentiation / negative regulation of JNK cascade / JUN kinase binding / 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 / 脱リン酸化 / プロテインチロシンホスファターゼ / negative regulation of cell migration / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / negative regulation of epithelial cell proliferation / response to lipopolysaccharide / 核質 / 細胞核 / 細胞質基質 / 細胞質
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
Chem-NV3 / 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: 3 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
組織認可番号国
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. / 年: 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8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 1.12022年11月23日Group: Data collection / カテゴリ: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
改定 1.22023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)106,76912
ポリマ－104,7006
非ポリマー2,0696
水0
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)17,7952
ポリマ－17,4501
非ポリマー3451
水0
タイプ名称対称操作数
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)17,7952
ポリマ－17,4501
非ポリマー3451
水0
タイプ名称対称操作数
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)17,7952
ポリマ－17,4501
非ポリマー3451
水0
タイプ名称対称操作数
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)17,7952
ポリマ－17,4501
非ポリマー3451
水0
タイプ名称対称操作数
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)17,7952
ポリマ－17,4501
非ポリマー3451
水0
タイプ名称対称操作数
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)17,7952
ポリマ－17,4501
非ポリマー3451
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)97.078, 100.045, 135.375
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
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 322 through 465)
d_2ens_1(chain "B" and resid 322 through 465)
d_3ens_1(chain "C" and resid 322 through 465)
d_4ens_1(chain "D" and resid 322 through 465)
d_5ens_1(chain "E" and resid 322 through 465)
d_6ens_1(chain "F" and resid 322 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_1LEUGLYA3 - 146
d_21ens_1LEUGLYC1 - 144
d_31ens_1LEUGLYE2 - 145
d_41ens_1LEUGLYG3 - 146
d_51ens_1LEUGLYI3 - 146
d_61ens_1LEUGLYK3 - 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, プロテインチロシンホスファターゼ
#2: 化合物
ChemComp-NV3 / 1-[(9-chlorobenzo[h]quinazolin-2-yl)sulfanyl]-3,3-dimethylbutan-2-one


分子量: 344.858 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C18H17ClN2OS / タイプ: SUBJECT OF INVESTIGATION
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: 3.24 Å3/Da / 溶媒含有率: 62.04 %
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
詳細: 100 mM HEPES, pH 7.0, 200 mM ammonium acetate, 25% w/v PEG3350

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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: NSLS-II / ビームライン: 17-ID-1 / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2017年3月20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: 0.9792 Å / 相対比: 1
反射解像度: 3→48.55 Å / Num. obs: 27028 / % possible obs: 99.75 % / 冗長度: 6.7 % / Biso Wilson estimate: 64.16 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.2099 / Net I/σ(I): 7.55
反射 シェル解像度: 3→3.107 Å / 冗長度: 6.6 % / Rmerge(I) obs: 1.211 / Num. unique obs: 2641 / CC1/2: 0.598 / % possible all: 98.65

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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
XDSデータスケーリング
PHASER位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 6MC1

6mc1


解像度: 3→48.55 Å / SU ML: 0.3514 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 21.9391
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2137 2009 7.43 %
Rwork0.1741 25012 -
obs0.177 27021 99.4 %
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: 65.31 Å2
精密化ステップサイクル: LAST / 解像度: 3→48.55 Å
タンパク質核酸リガンド溶媒全体
原子数7128 0 138 0 7266
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00327434
X-RAY DIFFRACTIONf_angle_d0.524910064
X-RAY DIFFRACTIONf_chiral_restr0.04071079
X-RAY DIFFRACTIONf_plane_restr0.00321299
X-RAY DIFFRACTIONf_dihedral_angle_d18.98362762
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.559541867543
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.479509702317
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.470462597563
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.459565238273
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.638010147235
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.3591320.32441640X-RAY DIFFRACTION92.73
3.07-3.150.3561480.26591758X-RAY DIFFRACTION99.95
3.15-3.250.30411380.24521789X-RAY DIFFRACTION99.9
3.25-3.350.29491420.23941763X-RAY DIFFRACTION100
3.35-3.470.28711450.23441788X-RAY DIFFRACTION99.95
3.47-3.610.22921410.20631755X-RAY DIFFRACTION99.95
3.61-3.770.26891420.21071777X-RAY DIFFRACTION99.84
3.77-3.970.21431380.16931792X-RAY DIFFRACTION100
3.97-4.220.18871430.15081788X-RAY DIFFRACTION99.95
4.22-4.550.17511470.13361794X-RAY DIFFRACTION100
4.55-50.15361470.12581796X-RAY DIFFRACTION100
5-5.730.19991440.14861813X-RAY DIFFRACTION99.9
5.73-7.210.21461460.17541840X-RAY DIFFRACTION100
7.21-48.550.14591560.1351919X-RAY DIFFRACTION99.43
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)
15.612394592460.4117286873232.510309835447.043847019343.870389826234.831778621940.23574298527-0.67214412083-0.2992695348550.927401290383-0.02877784165620.675722718560.519602172847-0.430624961509-0.196271948490.475941145125-0.06744378243180.01936427321740.4089360541680.08804374086330.390155620256-20.992328368913.7290982101-29.230599911
29.41672708642-0.313562561619-0.6042251324314.774639258371.118918111584.4145920950.153198427711-0.01991878284340.0847059101522-0.347284018743-0.0270075426608-0.0684142785746-0.309769586699-0.100355574099-0.1222256877790.397159055921-0.0183426866680.02646835388160.3397269819550.03352607651960.360918088665-13.1485260419.410812614-36.1994936213
35.06967852722.221424762242.391828544052.327413487340.4670296363175.210202876810.427623192747-1.014675352650.1080562692440.541865664298-0.381243307368-0.0505405832512-0.0388282746366-0.183975655056-0.07421505365140.589536249939-0.110338623636-0.002182358467430.4662361074170.009434888956740.44002371466-10.301196148420.5246873713-23.4622092051
47.33769078811-0.7078974504770.2647540802852.32222600310.3891397917184.474111506050.168118421739-0.1528247247040.5079256557390.271214165493-0.273741766074-1.15414826588-0.9199191123850.5045741609890.1990969455830.633328279873-0.100016122865-0.08047380570530.481905669439-0.03978057855060.4512585445291.6205973105626.8119910926-27.4997221942
57.19644523007-0.941039338741-1.054984584030.4675127506531.429706462325.99961352280.2702874494410.54604719736-0.721731759326-0.4217291655410.177068912471.382557574691.01895423227-0.771148886272-0.2940092449450.508312342891-0.0494467803141-0.1248968948760.4513392785550.002621743226190.39198657479-19.096823194438.9766845809-52.1462689569
64.78704542025-2.07495343296-4.367788281892.520691163261.264341557314.25940463693-0.139524493282-0.192167057865-2.450021001910.70362672733-0.2450140203710.754336077902-0.335566234773-0.5618297438490.7219713600611.39896081801-0.0363089415627-0.1033035876760.498342280366-0.01383757852940.945225668047-12.020357774627.7029364842-51.6165663865
71.601020487681.62757778871-2.477651067982.73048395384-4.488124724898.087611830150.5705536919991.78231515085-1.88256037351-1.67076069766-0.1827124670891.538201163641.8635880078-1.60940524332-0.3559451726390.961108627335-0.108351109927-0.2507612134830.75023116948-0.2072338749160.798187656532-15.950598365430.2844567931-61.3469320642
88.15746861893-5.94422189661.144083105184.96146721784-0.4890762099533.98264487679-0.1214888511210.307250105315-0.111525709231-0.837406636050.3522474935390.1663349143840.4302965328850.0350495703556-0.23714775270.489563545495-0.0588600937778-0.07718793701920.4388014542160.0777044024830.30809516859-6.8881681457435.1187908074-53.6822107695
94.671848083143.854202635494.186896380538.133742322142.40046662564.183990338440.1944515264290.7415474290160.106375664315-0.993100819527-0.374550678218-0.1813357664091.234549286550.5421822891250.1409565123710.7196222665430.1516340428050.03964375110240.6214264356150.0956811802660.406431585622-3.1842099559635.5774013646-59.5573046349
106.75391788303-3.50846855133-2.161143800648.147860847362.483359545092.164017802740.140727581605-0.4409165785170.07436005883251.11186821996-0.184876570424-1.123359601520.5940822771370.1947867491540.1608003504460.520677873846-0.0476904839693-0.07118065403970.4160332729640.03958381931710.474651795388-3.1539886737941.2525518979-38.0353558917
119.24334238453.066507773813.262648682099.077683377583.912224807542.24747392901-0.2984304269781.029058154651.59068754333-0.663260463615-0.782743008756-0.076224961813-0.0463065799360.169781498761.319362435250.416347927030.009191071516310.06013800690450.4595327194050.1026816761380.544927080224-8.6207872818649.3431104608-52.4686586621
126.88384604578-1.4063918381-0.8138663283945.685662799964.54930271229.3416191938-0.01123337841460.208034340450.09354753707160.083577957707-0.3532775193010.242470328227-0.365603150951-0.4032300490.2399294193820.291395022273-0.0179118708488-0.02159252634820.3182219620530.04210530947580.266809658093-13.307586967141.8410253624-47.3068390919
132.74302757435-0.334700191330.8566723828836.247637786513.346632138932.72578532462-0.380054785012-0.3025901960840.849959368719-0.322330811544-0.08404326760280.225655564833-0.506871919059-0.5169482485840.4578012590220.5405063632250.137789143110.0355139570320.5317750709520.005166072605980.636382553266-22.635561438447.7348632198-42.4571267076
149.538150592494.689543361278.505422555916.331085591133.095402516158.442794195220.76325044722-1.02945677222-1.255129820780.183016092591-0.223446835634-0.5481248446190.220604072381-0.821008882483-1.055581835540.445262436237-0.03308990159640.07494030260490.464139660570.1340797256890.605491718716-18.082372143435.8797695277-38.4898891524
153.70338264678-3.365323223194.923390876493.48781121438-4.613668897357.11834254726-0.147891971847-0.6503734988091.082341556431.0910923349-0.545799218763-0.155224543278-1.0014941851-0.2863136829450.7695511851180.7281080292660.0862310952658-0.07195072003520.578020623253-0.005500775171120.624253882924-12.133767521453.2986562382-36.5122166134
163.825253518395.513937597940.05625887959999.034100722930.7960796671116.8903763142-0.04196693546980.0243052690136-1.25139678861-0.373121269894-0.15251115252-0.2995909026710.3464343370590.7430383577260.2261894533760.4809563182820.1211088219290.01738884440220.5627627409-0.0275357054970.59827611470717.962214187624.0413818021-48.6321009571
176.64090456711-1.472472806430.5237267917196.64149390742-3.252629013325.666325231430.138368569477-0.107606089386-0.408910938257-0.263703656712-0.106082377582-0.2682295569590.5204942762090.0883628806728-0.01647510358330.4353709223760.03261978607720.009002623663310.3536172595720.03374333022980.373090250718.8801415937726.8097821081-43.5973334316
188.07111101693-0.93709926754-0.2776264098245.34505747583-3.79796137313.567965369760.0770993573865-0.3826289625540.7335350686040.4485459878680.0143733157151-0.408659296225-0.6603733473730.153325347375-0.1235243149050.577074377021-0.02388520990230.04856644768980.403607805659-0.05583506228990.43620249869215.784277848139.9305029489-47.9198966745
196.877428779410.372880949665-4.678149352542.23847869332-1.880042559845.374552163220.148998322096-0.210844539514-0.450104757052-0.0852446627221-0.227769178146-0.512752066132-0.04146192216340.6152985728010.1175507238780.5191675679240.02271052111060.06818810999790.394067717637-0.03610503323890.44580861135923.602410238632.8828896672-52.7458880066
205.346615373331.068628945395.264881669978.98945073738-0.2419267608515.48016633476-0.3754816396460.07707197920730.873755366806-0.7873723714740.204510613748-1.25949287195-1.735011282320.8903237790480.1957107182290.873003919933-0.148568397330.2935642305280.666051389881-0.005951655637620.78330671456625.626649240646.3912227039-55.1921165667
217.26729999718-2.602309808574.04006771834.4374055111-4.740093718045.81938314260.131066723893-0.143243668258-0.00567097425610.44244512868-0.134604258728-0.391502218195-1.348350153580.5908191800140.005029156554710.670556574384-0.005212665087840.06606285740740.568864177911-0.04239328370160.483244125967-18.076498002955.7094811665-9.07308636667
224.10489576491-0.39227726291-2.320672067656.73609497112-3.604334187757.213803258170.1413997138430.05215064001320.06325410824680.0707362064163-0.276491745196-0.677902881487-0.3295312080970.04768592310580.2299336367750.55822457170.05581832243010.03002719360420.56403051684-0.09985982761010.486632472066-22.166924586352.1755227258-2.6016405895
234.936900776252.39080549233.807715763154.313911991233.488426422413.747106698260.296716003120.287564698971-0.1872491029030.518131577464-0.290025119759-0.3126453151681.22953779339-0.62805411553-0.07968989765220.723276264181-0.05369632222710.1564715753740.4389888467790.01959011636840.44083184107-26.006098168143.9401945685-6.74298754111
241.189860031321.463706237360.3206056615049.54201555746.187847532244.51811969735-0.3657356474780.137220033612-0.1045010392830.0500283442773-0.2199453980521.57548873579-0.654993307086-1.84964037741.047634415680.5582335658230.1775278547510.02522672275291.17384928497-0.1347630656790.666917304743-33.834453580751.5950513675-13.5270232537
255.74228123117-1.95210351077-1.474537562673.785545088891.195925394559.31906647001-0.05392511264920.520584059814-0.424264701951-0.0293438803902-0.2513758816710.400642122533-0.390251778188-0.285489830270.2820192897320.3847812042540.05732286034270.07834205766990.569705680495-0.04927800566290.41095074919-23.78094201650.9605753147-14.9008034301
261.30924056534-0.7091096947561.336679025657.171137405021.33831982389.880265241120.02669044416480.197793242390.0210055672503-0.631691762611-0.1567228452760.0568357818773-1.07104692605-0.9802412782440.1388700934070.6454755897050.1089178774150.1235954554070.712787339497-0.03042028457080.437970992725-19.79650161553.8470668306-23.6749666792
273.33870799437-3.70628239909-0.9134249651647.84173438004-2.161729936492.92833082370.4673050856521.79314000049-0.57261855933-1.27700025942-0.2741902474241.07545184748-0.439750946076-1.62345719087-0.3378727557650.8344507984030.1242178573650.00410126729231.20592246846-0.1826190766440.625002758271-29.232098154345.1719609102-28.4188694546
285.82008695197-3.838194438952.155885628185.20745818184-5.52111135227.03367331717-0.6110932849610.3928171851450.479577013082-0.634315744259-0.0624752576578-0.665500073367-0.4668925638290.8984217079490.7824116201540.706401913108-0.22480387788-0.195075240850.5785056360620.1466435754530.83439897547624.85941445124.3861931491-10.9241830303
298.262442801560.392562321259-1.99385806034.661379610610.9344644207788.35336384543-0.17435200974-0.1524059370961.325959165430.05765942567530.12294350334-0.999827540812-0.5691962442550.958209477909-0.0655494988830.859499224109-0.187778762272-0.3181258056980.6363566498670.06050084658640.89645107297829.504819068926.3092985957-4.44518039987
303.05983118368-4.39663194583-1.501264874567.957563616862.915406302282.302204536190.8652193441-0.222988576655-1.15173148596-0.713751500115-0.238437165207-0.129459059873-0.769357899241-0.192004400843-0.7050233840220.770926501051-0.197632827506-0.2572780586110.5776694302930.15775557410.63319901490225.154168849413.0133498313-2.83217312025
312.903384220631.03534982676-0.6425470682626.08459717875-1.791549393375.0082704044-0.3937265567220.00450315997956-0.04843380309980.0814054071220.197968238584-0.4220364778970.0698197876782-0.1345046816820.1696523579720.774665183279-0.123656681918-0.2196659849890.5504773113840.0429210031970.53556011684919.945376438115.5998385428-0.669674573517
328.366060270742.23019891299-0.8304665665436.07421595056-2.838740743736.44342364869-0.0495870751349-0.6235745854041.587805009431.550354951040.3972136229450.267831103022-0.523000674993-0.321290475974-0.2106675285770.8749697681960.0560814722966-0.286946687890.690796470098-0.03767714371980.74620351650413.852233412626.43846116151.85387307456
336.33641040041-1.084294446083.111360406410.172684487728-0.7780865479773.57822222196-0.4772019848320.7037350962211.026743844470.694667610305-0.20943508836-0.169152256905-0.4052386090260.03758518610730.3576852750960.83329645011-0.251825949228-0.2088381487730.5857379804950.1136694846710.57627936370415.794723358423.6312959812-7.25253631787
347.904699047931.100222340312.865959465859.24941682848-1.334823441316.06341806808-0.5341664249570.1160009110130.840040850291-0.511511583437-0.129177651040.161645244355-0.389706401290.2331533306190.7148296406940.804948664238-0.187884449021-0.3015168380360.4954941661260.2188450605440.6903639439189.0556277752229.5713926086-15.1939392267
359.336602281946.13846931554-1.772715657194.12911733292-1.353358112110.791744183097-0.182110390616-1.428701522150.201648925723-1.58825555571-1.289103931440.2810160045560.3820001357271.214472706541.489926665520.695425139013-0.0917947165105-0.1947189886670.786095679940.05516100536440.55480559713915.05578968318.5345952836-18.1367748179
363.59253610566-4.72131317948-1.104446595267.597834306721.804477000868.47856738219-0.648225138860.0026278739731-0.6652631033650.4779075839960.4846292550151.1606571703-0.361145128709-0.684978702417-0.002402594413610.842944698316-0.22337712842-0.2051361633460.7945773143430.1079526573080.6484439087640.57317928760222.1954434034-7.66904356147
379.59950148836-2.71078506423-6.420014203167.444406672731.006600154694.29927526943-0.239044505164-0.469464880102-0.64473971102-0.440974558383-0.0492351630408-0.02914781411821.07650421460.3374339264410.3900516546140.615929593691-0.0847067962436-0.1359324712430.4443952583470.1086692282930.67847485564613.622680454845.0954533331-12.7363547654
385.706223278945.5942588582-0.3763135415045.819410122710.5518828340652.500234776510.689867761135-0.364038350721-0.3633170239670.0423346893058-1.096267430220.5759049754650.277025222423-0.2864525561.005215382570.912989060963-0.118330781095-0.25850955070.5465680014580.02561380533570.7762693927929.5465560469938.2036233739-20.4365497767
390.191493411656-0.6396257491260.01448001799331.91658056701-0.4866279555773.04104840189-0.366969692665-0.170723668422-0.0542683664734-1.212203493990.01462564914630.3813702405920.176664575596-0.2442215666130.3127750393910.575019497244-0.0730244484727-0.2328116342580.4744151731940.09586565822040.82417593919910.896380870451.032436226-20.5593737612
406.321164805594.145843009834.724888996894.895491111856.644519868779.497030091950.437054378071-0.13419651598-0.7045205663650.21305406565-0.617016703194-0.2708813618660.161441930136-0.4806103534370.4572171819940.610118965351-0.0616812954815-0.2505801470570.3919533553790.07171204940530.7473881489646.0812641147550.2837786961-25.4840011051
419.899316646174.040950853450.159646514854.256563210090.2887989110438.16859838569-0.0227728204090.0529112378740.1205689932950.183304500945-0.004811677608960.602332698931-0.550600169323-0.780811491626-0.06685798954960.4008298524960.0953614089895-0.1148812873430.4110255064540.05205209095080.6585102548257.4749664954160.0757363659-11.9656327324
420.7251189695390.241889912072.024767412193.609225670431.232307146345.281302865380.147817818241-0.2786266878860.07954433213970.313348646737-0.05123101582380.2124810129220.54392487551-0.122681412603-0.13897815810.395701522172-0.0298736433527-0.1106284766080.4986364451710.07292724321760.61584036167813.087594390553.163088798-4.73747404184
435.881128294595.28825986715-5.332119389687.30943020486-3.931185772845.374527821980.703242270709-0.1529635197741.245313723650.9433236067040.2206336165560.182551889875-0.70065067072-0.799994538702-1.080918330760.588201650735-0.0334924931168-0.05274393992870.655514402046-0.0345609611620.64170518428411.013917486565.95222264720.409940804229
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 320 through 362 )AA320 - 3621 - 43
22chain 'A' and (resid 363 through 400 )AA363 - 40044 - 81
33chain 'A' and (resid 401 through 448 )AA401 - 44882 - 129
44chain 'A' and (resid 449 through 467 )AA449 - 467130 - 148
55chain 'B' and (resid 322 through 333 )BC322 - 3331 - 12
66chain 'B' and (resid 334 through 339 )BC334 - 33913 - 18
77chain 'B' and (resid 340 through 345 )BC340 - 34519 - 24
88chain 'B' and (resid 346 through 362 )BC346 - 36225 - 41
99chain 'B' and (resid 363 through 372 )BC363 - 37242 - 51
1010chain 'B' and (resid 373 through 383 )BC373 - 38352 - 62
1111chain 'B' and (resid 384 through 400 )BC384 - 40063 - 79
1212chain 'B' and (resid 401 through 425 )BC401 - 42580 - 104
1313chain 'B' and (resid 426 through 441 )BC426 - 441105 - 120
1414chain 'B' and (resid 442 through 448 )BC442 - 448121 - 127
1515chain 'B' and (resid 449 through 466 )BC449 - 466128 - 145
1616chain 'C' and (resid 321 through 339 )CE321 - 3391 - 19
1717chain 'C' and (resid 340 through 372 )CE340 - 37220 - 52
1818chain 'C' and (resid 373 through 400 )CE373 - 40053 - 80
1919chain 'C' and (resid 401 through 448 )CE401 - 44881 - 128
2020chain 'C' and (resid 449 through 467 )CE449 - 467129 - 147
2121chain 'D' and (resid 320 through 339 )DG320 - 3391 - 20
2222chain 'D' and (resid 340 through 362 )DG340 - 36221 - 43
2323chain 'D' and (resid 363 through 383 )DG363 - 38344 - 64
2424chain 'D' and (resid 384 through 400 )DG384 - 40065 - 81
2525chain 'D' and (resid 401 through 425 )DG401 - 42582 - 106
2626chain 'D' and (resid 426 through 448 )DG426 - 448107 - 129
2727chain 'D' and (resid 449 through 466 )DG449 - 466130 - 147
2828chain 'E' and (resid 320 through 339 )EI320 - 3391 - 20
2929chain 'E' and (resid 340 through 353 )EI340 - 35321 - 34
3030chain 'E' and (resid 354 through 362 )EI354 - 36235 - 43
3131chain 'E' and (resid 363 through 383 )EI363 - 38344 - 64
3232chain 'E' and (resid 384 through 400 )EI384 - 40065 - 81
3333chain 'E' and (resid 401 through 426 )EI401 - 42682 - 107
3434chain 'E' and (resid 427 through 441 )EI427 - 441108 - 122
3535chain 'E' and (resid 442 through 448 )EI442 - 448123 - 129
3636chain 'E' and (resid 449 through 465 )EI449 - 465130 - 146
3737chain 'F' and (resid 320 through 339 )FK320 - 3391 - 20
3838chain 'F' and (resid 340 through 345 )FK340 - 34521 - 26
3939chain 'F' and (resid 346 through 362 )FK346 - 36227 - 43
4040chain 'F' and (resid 363 through 372 )FK363 - 37244 - 53
4141chain 'F' and (resid 373 through 400 )FK373 - 40054 - 81
4242chain 'F' and (resid 401 through 448 )FK401 - 44882 - 129
4343chain 'F' and (resid 449 through 466 )FK449 - 466130 - 147

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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