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- PDB-7u4o: 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: 7u4o
タイトルStructure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1-((9-propyl-5,6-dihydrothieno[3,4-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 / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine 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 / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine 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 JUN kinase activity / negative regulation of oligodendrocyte differentiation / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / JUN kinase binding / negative regulation of JNK cascade / positive regulation of regulatory T cell differentiation / negative regulation of stress-activated MAPK cascade / mitogen-activated protein kinase p38 binding / dephosphorylation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / oligodendrocyte differentiation / phosphatase activity / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / protein-tyrosine-phosphatase / 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 / nucleoplasm / nucleus / cytosol / cytoplasm
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 profile. / Dual specificity protein phosphatase domain / 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 profile. / Dual specificity protein phosphatase domain / 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-L8K / 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: 2.3 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)R01AR66003 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122473 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI055403 米国
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)R35MD122473 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2月28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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)106,86312
ポリマ－104,7006
非ポリマー2,1636
水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)17,8102
ポリマ－17,4501
非ポリマー3611
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)17,8102
ポリマ－17,4501
非ポリマー3611
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)17,8102
ポリマ－17,4501
非ポリマー3611
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)17,8102
ポリマ－17,4501
非ポリマー3611
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)17,8102
ポリマ－17,4501
非ポリマー3611
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)17,8102
ポリマ－17,4501
非ポリマー3611
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)65.990, 129.041, 84.118
Angle α, β, γ (deg.)90.000, 91.003, 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
11
21
31
41
51
61

NCSドメイン領域:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 320 - 464 / Label seq-ID: 5 - 149

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 320 through 464)AA
22(chain 'B' and resid 320 through 464)BB
33chain 'C'CC
44(chain 'D' and resid 320 through 464)DD
55(chain 'E' and resid 320 through 464)EE
66(chain 'F' and resid 320 through 464)FF

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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-L8K / 3,3-dimethyl-1-{[(9aM)-9-propyl-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one


分子量: 360.537 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C19H24N2OS2 / 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: 3.42 Å3/Da / 溶媒含有率: 64.04 %
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: 7.5
詳細: 100 mM Tris, pH 7.5, 200 mM sodium acetate, 35% 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: APS / ビームライン: 24-ID-E / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2017年7月7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: 2.3→48.52 Å / Num. obs: 62434 / % possible obs: 98.1 % / 冗長度: 3.3 % / Biso Wilson estimate: 39.92 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.07761 / Rrim(I) all: 0.09279 / Net I/σ(I): 11.69
反射 シェル解像度: 2.3→2.382 Å / 冗長度: 2.5 % / Rmerge(I) obs: 0.5556 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 13546 / CC1/2: 0.613 / Rrim(I) all: 0.6937 / % possible all: 86.01

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
Cootモデル構築
XDSデータスケーリング
PHASER位相決定
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

6mc1


解像度: 2.3→48.52 Å / SU ML: 0.3062 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.8723
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2378 2031 3.32 %
Rwork0.1993 59216 -
obs0.2005 61247 98.11 %
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: 45.62 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→48.52 Å
タンパク質核酸リガンド溶媒全体
原子数7213 0 144 0 7357
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00367529
X-RAY DIFFRACTIONf_angle_d0.639410187
X-RAY DIFFRACTIONf_chiral_restr0.04521088
X-RAY DIFFRACTIONf_plane_restr0.00411314
X-RAY DIFFRACTIONf_dihedral_angle_d17.25454487
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.30111170.29423249X-RAY DIFFRACTION80.99
2.35-2.410.32431300.2833892X-RAY DIFFRACTION97.95
2.41-2.480.30671420.27273995X-RAY DIFFRACTION99.73
2.48-2.550.25191310.26174023X-RAY DIFFRACTION99.69
2.55-2.630.27531410.25564013X-RAY DIFFRACTION99.62
2.63-2.730.29921350.25493960X-RAY DIFFRACTION99.34
2.73-2.840.31261330.26014007X-RAY DIFFRACTION99.69
2.84-2.970.35161370.25613987X-RAY DIFFRACTION99.59
2.97-3.120.2681430.26573993X-RAY DIFFRACTION99.02
3.12-3.320.28161330.23834005X-RAY DIFFRACTION99.54
3.32-3.570.28831330.21453997X-RAY DIFFRACTION99.42
3.57-3.930.22811400.18044007X-RAY DIFFRACTION99.42
3.93-4.50.17951330.1424006X-RAY DIFFRACTION99.02
4.5-5.670.16341410.13694012X-RAY DIFFRACTION99.45
5.67-48.520.16711420.14554070X-RAY DIFFRACTION99.18
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)
10.298984705661-0.687316802899-0.2981619814751.615705384130.7402571630316.9467723380.1929216302890.311449730301-0.1166474644940.00144064009160.04832266579190.1403144269390.201372819685-0.494098356252-0.07794590663890.313034324484-0.0300949843724-0.07527932081690.38457660738-0.03853473857470.38663556037-38.33690578568.10803015425-23.74180015
22.12284937756-1.36081990537-0.3630860427578.20712677686-3.00677010352.174477092060.57854271651-0.870009164210.0148205399759-0.13368231345-0.665287604770.338416207368-0.117578058452-0.06049989384650.2327195792790.379792790911-0.060401519460.0007125511273250.4790886156030.01295727325350.506456464515-37.616086364910.770069828-14.0488379049
36.82978277412-2.372852696744.162337943324.521248231270.4573574778663.509748522610.1255915707140.0326713464311-0.380938436165-0.3394567137290.3440609913161.415639860610.738072304707-0.842030208931-0.3346045924540.571247060361-0.111020383375-0.03242346019710.4496134466660.04136021258670.880527876345-39.0149415011-0.285356340097-17.0008663129
42.92705741451-1.116087933110.4869282726933.95032886319-0.01868411405044.473560541730.0216889828917-0.0152472365591-0.0987086818144-0.0361101849413-0.005823401223450.396311771442-0.1710036960580.0116017952502-0.06352531389640.2810508978870.0419608311376-0.03252278626950.2434930004980.03309661617590.346015553559-28.98348672147.63978095382-15.7323977185
51.583989986382.33205515329-0.7270560111253.34662747104-1.237918225852.526405701-0.121041518726-0.04471890499990.04339563338850.4284791467350.2767792804790.0880743035508-0.0450623211009-0.163436865611-0.1666530404990.2632574292360.0546693445373-0.0291878151980.2970002740850.008662281068750.335507179312-24.120504089411.8900875901-16.025354733
65.450360255554.135575530640.5595728771114.006947177260.3189233073761.67558762339-0.1840496982560.339434209518-0.400198754058-0.141441079070.301252407078-0.7594457702390.201572991910.119753441718-0.09635103910550.3477637871420.0143449650232-0.03557751080510.36443577659-0.02895538362370.373439235463-20.8518073577.40049125987-27.6086157322
71.02171213827-0.0315604214956-0.7060255876922.145697295440.2897713626832.5679711466-0.00385432606570.230306152654-0.0341149104044-0.118875018977-0.09974258729510.07594411213560.0433897015507-0.3667027248820.08654261304270.2526344330970.00873948445939-0.04875402840340.307044726206-0.001550580538880.334936876714-28.997546886712.755427477-26.0724250767
86.356539207010.3333731608220.5189853822452.46919935438-0.3980719083035.785128734560.003418832788370.4849611613990.0892443036802-0.527746373350.1660892295330.3756733739550.26337797388-0.328466918301-0.1612145548540.3642776478150.0210391141504-0.05518611548370.3079246047410.01905685236780.308087835353-34.452339329918.5206491539-32.7190612549
95.9830774631-4.71456561789-3.839763390378.138254035357.620259039939.569032086930.444782342310.7053495663070.534589967023-0.696182614109-0.303809321801-0.428961849587-0.399156558287-0.0533121002177-0.2186677141220.294854219726-0.0153002767131-0.02156507404910.317644650860.06034895080020.320245691048-21.169696019622.7022101518-34.6411355956
100.0308034784898-0.334138795014-0.04319659310413.709587516460.5525054585644.96251988638-0.07264708786350.3381069071581.248147104180.09980958874720.03085046970330.266678675889-0.243521337365-0.9193546469110.001028822420970.4393256559860.04582473358510.06856361158550.5527191572170.04834422119940.507297184297-16.09882995669.71899726842-57.4434142526
116.330162132380.745789011281-2.689954215785.70885816198-1.267690055016.808629390250.1756298879730.1997946897190.843081050615-0.2498855697650.1768691851020.391601612834-0.455888530805-0.557678963991-0.3776439128150.4422234865770.0502519557105-0.01902508634210.2992102581330.02389991588030.363952923243-17.46525534754.736309156-55.5023144204
126.995798287463.40191509823-3.053496570583.217728894050.2945924011614.9993883670.8840520916780.2860448025380.583095284173-0.242771321694-0.1595241054450.787878166787-0.920837704395-1.51657409876-0.7033503917120.5038351466640.0449979041363-0.01289857464610.5581079791520.02830651524970.255214971342-21.5389755283.28989496433-64.59636427
132.470519844371.73726857337-0.1719088712781.93764102331-0.3964111179151.997837881210.09034569747610.07290578660210.097709144445-0.0492507782213-0.001291743250460.0586181697214-0.0258592441260.00672538157209-0.1103766799880.3610636581340.030984140897-0.03560225635250.242790684197-0.008238730576680.293902022891-20.0944290909-2.74425462787-53.3856028448
144.83217527760.6348983664312.637564903191.452606619932.313133718797.680427117530.0477889510388-0.2338749442970.1910257259360.0690821001964-0.2189729652420.04981020193770.53041570074-0.478104532320.3004809895320.37738271305-0.0439207310018-0.006437094746670.2331876571110.04915672321040.270971712601-18.4797353929-5.12505691286-47.7106705657
150.3354824082330.5822427901060.6177043101181.131330147081.436013684367.12176869776-0.01041468881420.241978223313-0.154880324817-0.0570211000062-0.0336211825667-0.1946126621240.5401278326270.3398900609670.1399581465820.4665207124860.0945098139795-0.0154756690980.4061789652480.02477958856790.431336678973-6.53089513559-7.30094376497-51.832107918
161.31569526620.1846404452421.722234349460.384334765630.895215710184.174728074950.03106204294260.224562331055-0.0757810271916-0.07679343677660.0758126042085-0.1122124170730.05055458042180.233719687476-0.1199452324460.3926383461970.0209154722401-0.01022907246490.324304564626-0.009158516492450.358722207184-9.797202536251.57169524531-50.0236619689
177.469319136631.445426669481.969695353576.45837870315-1.469850876272.72226779461-0.152763562994-0.0842968406015-0.1385516501120.3375080704270.174391605858-0.2907935378170.001153667614880.5603886569680.03650313141310.383306627427-0.05154224299210.05556197206890.391142839013-0.04218004012460.272045820825-0.7027201826499.40380633697-49.0780608403
184.82311727648-2.184903105591.634901595494.73456315617-5.138088832835.6850425980.3346311608560.03613292559050.731988991948-0.155605743196-0.350174562485-0.144821894676-0.4358198767820.3209296466530.06362867506590.4203040296990.03358968270280.03130559164460.339132566012-0.05045777716260.395824832973-12.484226368311.9678232823-44.8831829762
195.78991152322-3.5728551643-5.189647089697.282293951144.154589046268.92530147812-0.30268906335-0.5489315763060.2486979939130.3430449337710.537593929484-0.9908487900330.3488520084350.995610680265-0.2547501682530.381812862703-0.0001653557126-0.05769630893910.52482275283-0.01600168661960.4119448360490.7020758925970.572890634127-38.8357630134
202.02101202875.76118227298-0.1945476368089.790223552870.9039444856353.94639147320.278216853638-1.33903062675-0.5326988312290.717409787438-0.469427596509-0.694040956595-0.0157737273712-0.409144396165-0.1958269869270.6799078423020.00805038204417-0.06938278835350.586636311848-0.1509699481610.333753445478-13.842713786416.731704471211.2158998352
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245.61109254191-0.903969890886-0.8689898494445.344815292241.505173864176.327632515-0.211412546947-0.2943940627940.7617666391130.3722489375380.03075599780470.327516242766-0.231322468819-0.237218248050.2364154784040.4322910055290.000988438750261-0.01835911567240.2943702171620.02906137474040.300540059445-23.214884260121.7810427566-4.06823443196
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264.50878215948-4.46544498968-2.331332191856.619865217993.698744064566.32115420051-0.0495004003565-0.1900454620630.657809252501-0.1697925482940.136732954951-0.728800264202-0.1886281815630.735347236666-0.1497187075560.415368528626-0.0468511771740.01172960135950.3500919407670.06234677184450.360726038559-6.88623100718.6859984668-3.39829074475
271.66582820454-1.27393221340.619965812693.39383389608-0.1659878709312.722533203480.0410598558765-0.05415541231180.269487219564-0.273205226922-0.026824725983-0.395710096213-0.2635911850170.1835080646820.01879731786580.381002373041-0.0260487042164-0.0007379885385760.2710916275510.02589322748650.342194393379-10.543914433613.17984156862.99105708439
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296.739190684294.966159624161.699167650578.03557796869-0.4396743728078.77686821721-0.2169645450260.62257165919-0.644107074447-0.448499311089-0.00370216303047-1.58902974260.3651917436661.076907588240.1009163244740.3075402240120.05964071142710.03149007848440.3570566939180.02507293726580.4780795830681.548055111534.22570864966-0.770246084565
303.60188996882-2.18538295049-0.0991282511643.159879193921.985431350521.79272261498-0.236534944685-0.2696552442970.01823380525210.3234539291840.144308404334-0.2123224187110.1425816609220.03524877635180.09347833237580.327156222452-0.0525378318935-0.03349183540810.404779899026-0.03646710486690.4566772704158.8143198696123.3837184002-15.3744354652
313.76834649425-0.3116757424014.641787099458.647987800632.75751079826.866184935710.258178869697-0.315548842430.4360672997470.849656415411-0.2137422985231.072210713211.12089311066-1.40535032464-0.07334295676090.446276326234-0.0758145080711-0.0320124385670.5386046365350.0271672024690.47937981965-6.1551247764227.3686761849-28.6984895509
326.0952171953-0.8610436217586.181492045492.70471857667-1.224629207016.51509376922-0.09891632501950.3537969592260.717395552607-0.401845355829-0.0366699174965-0.522917087575-0.06746419656370.6509964847510.0861721675820.382512740837-0.03145475941050.0621598276570.4397236406730.0288571315340.51754978761211.179576608929.4703316671-30.1616628875
331.972625365110.9480125961480.8016846255983.95530385641.205105112653.075049548620.03318644211290.1401377500070.0697840273404-0.007993330406730.00301802792502-0.0525235452290.224640038692-0.00402044248459-0.09302122640020.267840518009-0.02300141236740.003312052247230.3807071238310.009699369704110.3667614646026.9113724879917.1261097704-28.6337623065
341.938207287410.79777644468-3.428150332915.883973488550.5688030575048.91520435288-0.0824558154270.8105378755230.11642440652-1.149453983360.19817741411-0.19713307664-0.4414400314430.444964498758-0.08595805009090.393669398185-0.0671200533078-0.04959417137830.481229993223-0.007200324304150.4633181630011.8964895441221.2681990398-40.8582460658
358.041665354010.0912307128606-1.998711599351.686377680471.258108106852.6435122798-0.571327358298-0.9829897582510.1609519766291.27789599-0.0382340133198-0.05762738252670.01965371066170.2160925257490.3599930628930.6354437779730.04480647886660.0815088039190.63024159827-0.07571806053160.557834742534-12.987497348644.2447543594-0.758157324844
365.86466733279-1.944607693551.09293529282.4556137121-1.293616376026.58794540670.104976158004-0.4804950342330.1457393975980.245052519904-0.3147485403660.2586871546320.6884698363360.0758907368490.09830960543570.352683362385-0.07301914018990.01712013230350.404464952457-0.04231363502080.453890509779-11.249318038541.8368527683-5.54586802449
373.71446736960.232216834476-2.564896901023.82771977533.10292455414.68113115511-0.175542511593-1.022286733420.2000464748570.554044185310.08423386254120.8763322111210.08947744938170.2872860912190.01948181521420.451219068781-0.1155655513540.01331383634670.613550636381-0.04952782077350.655248484325-18.749390203935.296781644-4.02504425865
382.69234086005-0.333383246327-1.586145416335.4482201976-0.3123723583952.63079322511-0.1942952211970.3881413920670.1309028189770.07564226260190.115663222417-0.0331677654754-0.1950038413760.03184623791250.06336271067080.30572790574-0.0622975982707-0.05044833107590.299517661912-0.04376181020040.357653290421-8.8667482704637.3986972795-11.9128886715
395.916576829993.79743128101-2.388372482674.4264820051-2.133393053622.99399646570.2031481301950.0680710642224-0.06551722028130.384508858303-0.037447662769-0.0685005320715-0.0419937844550.295504138602-0.1261824575090.368559933017-0.014104888249-0.05502146114560.357389948098-0.107152793510.416865084135-4.1622854289739.6935497057-15.6698822225
401.931458194863.34929553252-1.803141247856.84079339352-1.137935903054.927851973140.2513302725090.8843408283060.253878115433-0.7251984419720.3238050677860.8677254701-0.307101175613-0.446461389956-0.570736569030.483342019346-0.0432727895987-0.08812321568840.4989252331340.003531901769730.568165176198-11.649968029848.3708963447-21.0042231681
413.504538607831.665039406990.8131378643485.13150642286-0.8312292399992.30212633928-0.0899176645710.199014864702-0.1892885879870.08306718807270.1784253461230.2851810813760.0113269958265-0.0461877864122-0.09425769759080.36095266226-0.0435537744137-0.05701807967330.364814586552-0.05610722593070.415922044959-9.4554974454549.1956680617-12.0618946685
422.55767565040.414346203533-1.12523050485.6103133746-0.2812759817373.734462569240.1469761362080.04117201959240.3149217596360.197687386678-0.1731348674080.632747341795-0.46789951715-0.08787960601920.04140589503450.361987855067-0.05395198097-0.01076768511270.370898977183-0.09221705365990.482276232896-7.2669837063657.4102446618-5.35330060975
436.78711638117-2.468637852263.215938805188.13369862762-2.583149153688.302832418050.1199160017150.404767138280.641268138242-0.376011728875-0.1030303177780.139701033336-0.7382844455160.4312680223930.0291931551440.445190090455-0.06169894758460.02679326880470.400384286149-0.02597152493990.53519595152-1.5638206238961.1584649981-17.7370186985
446.258353729691.92955543922-2.671615670575.856993202352.941483446564.967715995660.290205283018-0.09193390654270.17283693682-0.504090955630.252300734162-0.699675489424-0.3882750834490.221504601189-0.3981165609450.5091689911540.1429632540860.1513809700610.5391640323960.08525916281670.4550813916-21.852421241945.4410807004-45.3691217454
458.55838110968-0.738784343001-0.2401472660912.367652684160.7291246604342.258773450436.95628847516E-5-0.119059916570.5312818831970.0238206023865-0.357789439838-0.8381681279050.7390787682220.5912770376530.4650068355790.485986003393-0.00337738569773-0.01149693162930.3386901099760.07708633568130.405085039053-25.548597548850.0555947922-43.5111907242
469.78146933454-6.24404326675-1.315198768764.629755664672.04293362132.62028535455-0.17324217062-0.07525514682650.3941976241280.169358532248-0.632565871697-2.09181214459-0.1757865680781.130830057020.7099657755160.5776975889740.02850798451070.02884723411250.6020251285110.1999112516830.772253868291-21.379487274857.1272526987-49.1954147627
471.62795705569-0.356895635732-1.107198422463.91958885789-0.2154435468544.188153745980.129765189834-0.205667322809-0.0567492299604-0.0892527726351-0.208317087013-0.0499925743303-0.08552897811680.4184618036590.08512452945130.3738375285940.0309307036599-0.02121149559590.3228030823330.06139739421190.300526511977-32.624658692254.0422564041-43.4981221939
484.201574582461.02219256494-3.460027379395.84253504245-3.014055555727.1017997218-0.0998544367262-0.169250147632-0.0743586063602-0.626383151679-0.0856629230679-0.2918968448380.3546399895820.6927718520710.1195501100150.3157297195460.04632023048570.004981718337680.2909803283090.0231359021230.307937185101-34.826702372258.8866046887-47.665812635
492.072112080741.57477647064-2.586817617128.833580186360.08754892165938.308726025620.0609654134163-0.401450247929-0.06356712879560.933139503066-0.1255846283240.0968969996726-0.521476894892-0.05052059493520.03813662075130.3571318467090.03554473115180.04160507991830.3524776920860.04224354515330.284689925312-40.934716929842.9423239725-33.499071823
506.427014900243.62903128385-2.774996748187.4357797859-2.923300894332.47261186003-0.5371669972961.15932950429-0.343105292432-1.082246174790.2818447558560.5116517303050.252138331081-1.15221059080.2017013467140.6225956309310.0509374385827-0.09810891742220.459389966673-0.02516064849220.410692176961-39.247194807343.1692918137-50.4125410215
511.716817699670.4159563565790.06122758019447.122451067910.09052019855860.3289223264920.03263315697760.2594847186170.0773986986467-0.31934367355-0.0269367342312-0.3940512517350.1110326843110.08389831422220.01692165208670.385386013450.0499621818195-0.01429824545880.3611713798030.05892988842170.370853288669-31.931113448842.8291325048-44.6654294674
523.84816637318-0.232236579101-1.962308774567.862792384211.024769193471.35399328403-0.02785433843590.0137635339685-0.153383150854-0.449121407542-0.179686171853-0.6799347108440.4582480208580.3630817768590.1361519094940.374949814640.0832588869997-0.02779643163450.3999502185880.1043821062640.378718673939-26.154505050634.266158162-41.4085074224
535.41039975733-0.556381421305-0.4189553256338.252028091215.730020897194.592545327730.05440604808310.109711640115-0.659199584325-0.145505262545-0.4417049709291.073827941780.835461485882-0.5248666801060.4298460907640.5321121139830.0375409795447-0.02639124814340.391237862470.01974216059510.451711033008-39.578835887329.7543104242-40.7743779131
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 317 through 332 )
2X-RAY DIFFRACTION2chain 'A' and (resid 333 through 339 )
3X-RAY DIFFRACTION3chain 'A' and (resid 340 through 345 )
4X-RAY DIFFRACTION4chain 'A' and (resid 346 through 362 )
5X-RAY DIFFRACTION5chain 'A' and (resid 363 through 383 )
6X-RAY DIFFRACTION6chain 'A' and (resid 384 through 400 )
7X-RAY DIFFRACTION7chain 'A' and (resid 401 through 426 )
8X-RAY DIFFRACTION8chain 'A' and (resid 427 through 448 )
9X-RAY DIFFRACTION9chain 'A' and (resid 449 through 466 )
10X-RAY DIFFRACTION10chain 'B' and (resid 318 through 326 )
11X-RAY DIFFRACTION11chain 'B' and (resid 327 through 339 )
12X-RAY DIFFRACTION12chain 'B' and (resid 340 through 345 )
13X-RAY DIFFRACTION13chain 'B' and (resid 346 through 362 )
14X-RAY DIFFRACTION14chain 'B' and (resid 363 through 383 )
15X-RAY DIFFRACTION15chain 'B' and (resid 384 through 400 )
16X-RAY DIFFRACTION16chain 'B' and (resid 401 through 426 )
17X-RAY DIFFRACTION17chain 'B' and (resid 427 through 441 )
18X-RAY DIFFRACTION18chain 'B' and (resid 442 through 448 )
19X-RAY DIFFRACTION19chain 'B' and (resid 449 through 466 )
20X-RAY DIFFRACTION20chain 'C' and (resid 320 through 328 )
21X-RAY DIFFRACTION21chain 'C' and (resid 329 through 339 )
22X-RAY DIFFRACTION22chain 'C' and (resid 340 through 345 )
23X-RAY DIFFRACTION23chain 'C' and (resid 346 through 362 )
24X-RAY DIFFRACTION24chain 'C' and (resid 363 through 372 )
25X-RAY DIFFRACTION25chain 'C' and (resid 373 through 383 )
26X-RAY DIFFRACTION26chain 'C' and (resid 384 through 399 )
27X-RAY DIFFRACTION27chain 'C' and (resid 400 through 426 )
28X-RAY DIFFRACTION28chain 'C' and (resid 427 through 448 )
29X-RAY DIFFRACTION29chain 'C' and (resid 449 through 464 )
30X-RAY DIFFRACTION30chain 'D' and (resid 317 through 372 )
31X-RAY DIFFRACTION31chain 'D' and (resid 373 through 383 )
32X-RAY DIFFRACTION32chain 'D' and (resid 384 through 399 )
33X-RAY DIFFRACTION33chain 'D' and (resid 400 through 448 )
34X-RAY DIFFRACTION34chain 'D' and (resid 449 through 466 )
35X-RAY DIFFRACTION35chain 'E' and (resid 318 through 326 )
36X-RAY DIFFRACTION36chain 'E' and (resid 327 through 339 )
37X-RAY DIFFRACTION37chain 'E' and (resid 340 through 345 )
38X-RAY DIFFRACTION38chain 'E' and (resid 346 through 362 )
39X-RAY DIFFRACTION39chain 'E' and (resid 363 through 383 )
40X-RAY DIFFRACTION40chain 'E' and (resid 384 through 399 )
41X-RAY DIFFRACTION41chain 'E' and (resid 400 through 427 )
42X-RAY DIFFRACTION42chain 'E' and (resid 428 through 448 )
43X-RAY DIFFRACTION43chain 'E' and (resid 449 through 466 )
44X-RAY DIFFRACTION44chain 'F' and (resid 320 through 326 )
45X-RAY DIFFRACTION45chain 'F' and (resid 327 through 339 )
46X-RAY DIFFRACTION46chain 'F' and (resid 340 through 345 )
47X-RAY DIFFRACTION47chain 'F' and (resid 346 through 362 )
48X-RAY DIFFRACTION48chain 'F' and (resid 363 through 372 )
49X-RAY DIFFRACTION49chain 'F' and (resid 373 through 383 )
50X-RAY DIFFRACTION50chain 'F' and (resid 384 through 399 )
51X-RAY DIFFRACTION51chain 'F' and (resid 400 through 426 )
52X-RAY DIFFRACTION52chain 'F' and (resid 427 through 448 )
53X-RAY DIFFRACTION53chain 'F' and (resid 449 through 466 )

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万見について

-
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

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