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- PDB-9s6b: Aeropyrum pernix acylaminoacyl peptidase co-crystallized with mer... -

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基本情報

登録情報
データベース: PDB / ID: 9s6b
タイトルAeropyrum pernix acylaminoacyl peptidase co-crystallized with meropenem.
要素Acylamino-acid-releasing enzyme
キーワードHYDROLASE / serine protease / HbPG / ligand binding
機能・相同性
機能・相同性情報


acylaminoacyl-peptidase / omega peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm
類似検索 - 分子機能
: / Acylamino-acid-releasing enzyme-like, N-terminal domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
類似検索 - ドメイン・相同性
(2R,2'R)-3,3'-oxydipropane-1,2-diol / Acylamino-acid-releasing enzyme
類似検索 - 構成要素
生物種Aeropyrum pernix K1 (好気性超好熱古細菌)
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Harmat, V. / Takacs, L. / Kiss-Szeman, A. / Banoczi, Z. / Jakli, I. / Hosogi, N. / Traore, D.A.K. / Perczel, A. / Menyhard, D.K.
資金援助European Union, ハンガリー, 4件
組織認可番号国
European Regional Development FundVEKOP-2.3.3-15-2017-00018European Union
Hungarian National Research, Development and Innovation Office2018-1.2.1-NKP-2018-00005 ハンガリー
European Regional Development FundRRF-2.3.1-21-2022-00015European Union
Hungarian National Research, Development and Innovation Office2020-1.1.6-JOVO-2021-00010 ハンガリー
引用ジャーナル: Protein Sci / 年: 2025
タイトル: Ligand binding Pro-miscuity of acylpeptide hydrolase, structural analysis of a detoxifying serine hydrolase.
著者: Anna J Kiss-Szemán / Luca Takács / Imre Jákli / Zoltán Bánóczi / Naoki Hosogi / Daouda A K Traore / Veronika Harmat / András Perczel / Dóra K Menyhárd /
要旨: Acylpeptide hydrolase (APEH) or acylaminoacyl-peptidase (AAP) is a serine hydrolase that regulates protein metabolism. It can also bind to and process unusual substrates, acting as a detoxifier. To ...Acylpeptide hydrolase (APEH) or acylaminoacyl-peptidase (AAP) is a serine hydrolase that regulates protein metabolism. It can also bind to and process unusual substrates, acting as a detoxifier. To better understand its promiscuous specificity, we determined the cryo-EM structures of mammalian APEH complexed with classical serine protease partners: a chloromethyl-ketone (CMK) inhibitor, an organophosphate (OP) pesticide (dichlorvos), and benzenesulfonyl-fluoride. Since CMK derivatives of N-acetylated peptides were suggested to induce apoptosis by inhibiting APEH, while OP complexes may serve as biomarkers of OP exposure and are linked to cognitive enhancement, these complexes carry physiological significance. We identified a unique strand-breaker Pro residue in the hydrolase domain, which relaxes the active site into a partially inactivated but more spacious conformation, transforming the classical serine protease apparatus into a versatile yet potent hydrolysis center with broad specificity, distinguishing the mammalian enzyme not only from other APEHs but also from serine α/β hydrolases sharing essentially the same fold.
履歴
登録2025年7月31日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年10月22日Provider: repository / タイプ: Initial release

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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: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
C: Acylamino-acid-releasing enzyme
D: Acylamino-acid-releasing enzyme
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)252,7577
ポリマ－252,2584
非ポリマー4993
水4,522251
1
A: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)126,2953
ポリマ－126,1292
非ポリマー1661
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Acylamino-acid-releasing enzyme
D: Acylamino-acid-releasing enzyme
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)126,4614
ポリマ－126,1292
非ポリマー3322
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)71.042, 98.283, 98.902
Angle α, β, γ (deg.)105.510, 103.190, 100.390
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,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 5 through 7 or (resid 8...
d_2ens_1(chain "C" and (resid 5 through 37 or resid 39...
d_1ens_2(chain "B" and (resid 6 through 53 or resid 55...
d_2ens_2(chain "D" and (resid 6 through 31 or (resid 32...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETLEULEUAA5 - 375 - 37
d_12ens_1VALVALSERSERAA39 - 8439 - 84
d_13ens_1GLNGLNVALVALAA89 - 9589 - 95
d_14ens_1THRTHRGLYGLYAA97 - 12197 - 121
d_15ens_1ALAALATHRTHRAA123 - 127123 - 127
d_16ens_1ASPASPASPASPAA132 - 140132 - 140
d_17ens_1LEULEUPROPROAA144 - 151144 - 151
d_18ens_1PHEPHEVALVALAA153 - 278153 - 278
d_19ens_1ALAALALEULEUAA280 - 351280 - 351
d_110ens_1SERSERALAALAAA353 - 427353 - 427
d_111ens_1TRPTRPALAALAAA429 - 554429 - 554
d_112ens_1ILEILEARGARGAA558 - 581558 - 581
d_21ens_1METMETLEULEUCC5 - 375 - 37
d_22ens_1VALVALVALVALCC39 - 9539 - 95
d_23ens_1THRTHRGLYGLYCC97 - 12197 - 121
d_24ens_1ALAALATHRTHRCC123 - 127123 - 127
d_25ens_1ASPASPASPASPCC132 - 140132 - 140
d_26ens_1LEULEUVALVALCC144 - 278144 - 278
d_27ens_1ALAALALEULEUCC280 - 351280 - 351
d_28ens_1SERSERALAALACC353 - 427353 - 427
d_29ens_1TRPTRPARGARGCC429 - 581429 - 581
d_11ens_2PROPROGLYGLYBB6 - 536 - 53
d_12ens_2GLUGLUHISHISBB55 - 7155 - 71
d_13ens_2GLYGLYGLYGLYBB73 - 16873 - 168
d_14ens_2PHEPHELEULEUBB170 - 187170 - 187
d_15ens_2VALVALLEULEUBB189 - 233189 - 233
d_16ens_2LEULEUALAALABB235 - 263235 - 263
d_17ens_2ARGARGSERSERBB265 - 481265 - 481
d_18ens_2ALAALAVALVALBB483 - 509483 - 509
d_19ens_2ARGARGGLUGLUBB511 - 580511 - 580
d_21ens_2PROPROHISHISDD6 - 716 - 71
d_22ens_2GLYGLYTHRTHRDD73 - 13073 - 130
d_23ens_2ARGARGGLYGLYDD133 - 168133 - 168
d_24ens_2PHEPHELEULEUDD170 - 187170 - 187
d_25ens_2VALVALLEULEUDD189 - 233189 - 233
d_26ens_2LEULEUALAALADD235 - 263235 - 263
d_27ens_2ARGARGTHRTHRDD265 - 493265 - 493
d_28ens_2SERSERVALVALDD496 - 509496 - 509
d_29ens_2ARGARGGLUGLUDD511 - 580511 - 580

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.123801115633, -0.624962258735, -0.770775881125), (-0.62263146839, -0.653740960863, 0.430061403361), (-0.772659911176, 0.426667237138, -0.470055029135)-20.1135602165, 16.7010081151, -38.308612502
2given(0.124305356438, -0.642437526366, -0.756189264059), (-0.624659229004, -0.642793449599, 0.443415638846), (-0.770940351766, 0.417241663631, -0.481207198771)-20.020920151, 16.2674776111, -38.0452921907

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要素

#1: タンパク質
Acylamino-acid-releasing enzyme / AARE / Acyl-peptide hydrolase / APH / Acylaminoacyl-peptidase


分子量: 63064.543 Da / 分子数: 4 / 変異: D524A / 由来タイプ: 組換発現 / 詳細: D524A active site mutant
由来: (組換発現) Aeropyrum pernix K1 (好気性超好熱古細菌)
遺伝子: APE_1547.1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9YBQ2, acylaminoacyl-peptidase
#2: 化合物 ChemComp-1AX / (2R,2'R)-3,3'-oxydipropane-1,2-diol


分子量: 166.172 Da / 分子数: 3 / 由来タイプ: 天然 / 式: C6H14O5
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 251 / 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N
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: 2.48 Å3/Da / 溶媒含有率: 50.44 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5
詳細: Reservoir: 0.45mM EDTA, 33mM sodium acetate buffer pH=5.0, 1.2% PEG Mw 4000; Protein solution: 0.24 mM in 20mM Tris pH=8.0, Meropenem solution: 62.5mM in methanol. Drop content: ...詳細: Reservoir: 0.45mM EDTA, 33mM sodium acetate buffer pH=5.0, 1.2% PEG Mw 4000; Protein solution: 0.24 mM in 20mM Tris pH=8.0, Meropenem solution: 62.5mM in methanol. Drop content: reservoir/protein/meropenem solutions= 1/1/0.5 volume ratio. Crystals were soaked in 30%w/w HbPG solurion saturated with meropenem.

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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: PETRA III, EMBL c/o DESY / ビームライン: P13 (MX1) / 波長: 0.9763 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年12月5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: 0.9763 Å / 相対比: 1
反射解像度: 2.3→40 Å / Num. obs: 105834 / % possible obs: 98.1 % / 冗長度: 3 % / Biso Wilson estimate: 62.56 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.081 / Net I/σ(I): 9.36
反射 シェル
解像度 (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
2.3-2.361.0575650.5021.022195
2.36-2.421.3673180.6540.775194.2
2.42-2.491.5870580.750.637193.8
2.49-2.572.1572310.7820.726197.9
2.57-2.662.7571020.8610.582199.5
2.66-2.753.5768530.9170.433199.5
2.75-2.854.4466440.940.34199.6
2.85-2.975.6763700.9660.255199.8
2.97-3.17.1960950.9790.189199.5
3.1-3.259.5458260.9890.138199.4
3.25-3.4311.8755520.9920.101199.4
3.43-3.6414.0952240.9950.082199.2
3.64-3.8916.4849020.9950.07198.9
3.89-4.219.5945500.9960.059198.8
4.2-4.622.6341880.9950.053198.9
4.6-5.1424.5538290.9960.05198.8
5.14-5.9423.8833470.9960.049199
5.94-7.2723.828300.9960.051199.1
7.27-10.2927.2721790.9970.046198.6
10.29-4027.111710.9940.047196.5

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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: 2.3→39.22 Å / SU ML: 0.3741 / 交差検証法: FREE R-VALUE / σ(F): 1.95 / 位相誤差: 28.3786
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2286 2101 1.99 %
Rwork0.1968 103689 -
obs0.1974 105790 98.21 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 69.92 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→39.22 Å
タンパク質核酸リガンド溶媒全体
原子数16639 0 23 251 16913
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002517100
X-RAY DIFFRACTIONf_angle_d0.562123285
X-RAY DIFFRACTIONf_chiral_restr0.04422659
X-RAY DIFFRACTIONf_plane_restr0.00423048
X-RAY DIFFRACTIONf_dihedral_angle_d11.68516006
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.500927084113
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.480495060564
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.36781290.37446684X-RAY DIFFRACTION94.85
2.35-2.410.34651510.3446579X-RAY DIFFRACTION94.48
2.41-2.480.33581360.31646629X-RAY DIFFRACTION94.1
2.48-2.550.35931360.29696777X-RAY DIFFRACTION96.16
2.55-2.630.29541480.28057063X-RAY DIFFRACTION99.72
2.63-2.730.29751580.25846993X-RAY DIFFRACTION99.61
2.73-2.840.31831510.24336999X-RAY DIFFRACTION99.71
2.84-2.970.2611580.23897024X-RAY DIFFRACTION99.82
2.97-3.120.29981560.2366965X-RAY DIFFRACTION99.68
3.12-3.320.30321310.22487007X-RAY DIFFRACTION99.47
3.32-3.570.2411300.19957029X-RAY DIFFRACTION99.27
3.57-3.930.22051260.18637004X-RAY DIFFRACTION99.17
3.93-4.50.15261230.15556991X-RAY DIFFRACTION99.07
4.5-5.670.18411320.1476969X-RAY DIFFRACTION99.09
5.67-39.220.16721360.16376976X-RAY DIFFRACTION99
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)
10.0910883290810.27595813835-0.03773244405620.409929143097-0.3693020421990.596541835090.0374749095061-0.1390338176120.1161172564810.889621777274-0.17415773581-0.3431708129520.155129674949-0.149494030472-3.40553974345E-70.695142462276-0.0417471830179-0.07565628178920.4938473482980.01386890128040.586475502722-4.80650792064-20.139387873912.8768259358
21.77032826719-0.2865721375710.4386977911441.617589341550.550750235221.83652032881-0.1882653929010.08512389946430.287936513631-0.176283190141-0.0418509225647-0.0928805647715-0.1001299318110.3349132027241.55042502629E-60.579402269091-0.06855457682890.01731958505730.5008682663210.06010556757390.5254833560760.309345978411-32.4070201407-3.85944018387
31.54867047360.230696419537-0.4022039711940.365526158820.847822150351.37515296391-0.3254463293280.1841971182120.0295437000404-0.4439824954060.02736993592450.345435792776-0.1236736287-0.2727807915063.48011159666E-50.637072895657-0.00841284871339-0.1027782494650.5199945226740.0147839076140.543097415961-19.4762385579-35.7396451528-12.5844203142
40.7692210631840.2194185326050.2499519406280.575803450172-0.1774174779180.736786742969-0.087755344468-0.1730357396720.09632200013330.114126585745-0.1122999348650.30058128412-0.0267015416894-0.445844942396-5.02083496702E-50.5200264732340.0317217224736-0.03955227516190.576191825225-0.02813317819290.568297104717-22.8085753208-29.27763530768.33749568272
50.8573505928371.185321043520.5251373295912.84940649224-0.05827887564910.117395739632-0.235347429330.2824209565580.199744149682-0.3291245459840.09291616845470.310205773692-0.202082079639-0.106707559041-1.14777166358E-50.7106007161060.151896683135-0.2082834570230.64351233607-0.02344807544290.715207213533-19.6054237778-6.81751363925-3.33222785901
61.144718528611.19183304747-0.6827668234520.929586146528-0.5313073505271.07368243872-0.1195666516240.468525453987-0.108832428286-0.1722801724670.138306554913-0.03713018498560.03924628123130.233141867199-5.09892371508E-50.8198461557080.0868642961892-0.2304530916890.658806127297-0.03514112957180.701277096351-4.99253822494-2.30027175134-1.36213242156
70.604067178113-0.5293962791270.01326082745510.463205018421-0.6218987830931.532198156810.248552836107-0.0757884242006-0.2867418002250.131931267375-0.1774627388880.3830364269150.251991642775-0.13049240417-4.32199968527E-60.494969618463-0.00841603126919-0.02318504736370.504385486947-0.0451006563780.629843911487.5702661548314.515153826226.6258794867
81.18339732566-0.534831222732-0.3137600648221.56079643682-0.6841290091730.7253784797830.110161554402-0.0221697991389-0.0384775264874-0.103022226235-0.1141581557320.39384089329-0.173496355419-0.287802848532-6.05207403338E-50.4803048212890.03164015765270.06509709430050.508514174415-0.05849555459540.6435123119872.4349627072835.98889703123.3420577921
91.944560330410.254007304383-0.08255557910150.8260681591380.2298228664150.957368100140.1261344129350.2530428035950.307008447962-0.12972771806-0.184536787597-0.0792150508002-0.2808503571950.184483403171-7.93823598771E-50.5501716025690.002300570212910.1032413752040.5797098905950.05005765891720.50342868235723.691560869340.18490527315.8907772985
102.144045119480.6176242638640.8437292359051.20165321420.3760684365151.574937612220.2349686541480.169269410111-0.2599312987940.183176605958-0.0443175020702-0.1592293604530.2534079383310.4248317185930.0001735163205980.5353799306470.02374522915330.006763613810840.536888532162-0.01719267533120.50517017332224.094057123918.197073129125.9311525794
111.901850810850.4520209398741.18445655110.6513950272920.5472240980021.205244566470.3205792984810.931880458723-0.563153205496-0.0131383787740.286568674351-0.3309373787850.2068889309350.8299676819620.04453096685250.5660336871460.218544815377-0.04655773755390.957363252409-0.2854968113050.69858893057224.51606512228.553939512425.94530533301
123.732018540771.509138557950.1862724047811.817185719130.3535431625370.824590604815-0.2292987701421.82629568438-0.201986500641-0.3421135109530.319116217358-0.09919597688770.1662470640770.6747802202010.2315590551550.8039989798070.101134840573-0.07869417743351.25022388745-0.1739191933850.62217861987214.87240390247.71153661136-6.32097118562
131.86232885090.680130716242-0.2284588982050.22504469676-0.2968207084321.088971386710.250373541810.644753103395-0.310489059461-0.2868773739550.2605804082520.1106016431060.207048815506-0.0854811296169-0.0002448640938030.7418853510970.136724718919-0.158399223360.723683986309-0.1544685049840.7003887507225.3695982631.984956857320.50424304053
140.0930888347848-0.120053796560.1601888179280.501432462917-0.9549102756770.673789933904-0.1660821783010.707213067375-0.0218281257236-0.2796746977440.2363240301450.03038676971610.115102317458-0.0866890141270.0002003720855870.598573054863-0.03704798565240.02436111718460.584424896781-0.03584946471770.595323121413-17.813376542838.5747416963-49.2665148571
151.67191117752-0.665905173149-0.06694397124062.08390942727-0.1720425832312.781139205060.3104366316990.104713064943-0.2466010269180.153541996015-0.132502322989-0.6125089489680.545198816620.978050319658-0.0001374257630940.5649521582990.0552044715137-0.082156851080.8998301949380.02002352886410.8091802593285.6635193573741.811137614-43.1314869593
161.37722421732-0.03282584597050.1159717253771.59482600813-0.3893001603031.867749298630.0581670659616-0.09840184055890.1934943449660.174746767058-0.0641226893267-0.0999087732797-0.2273944695240.352099754263-1.46528516942E-50.552554996758-0.1469348888940.0249535523910.5884682844980.05446018915930.476243203769-6.9470781968456.4757843525-39.8261073667
171.151523772330.8558533518090.4024280907693.557894536850.845708879232.369937106580.00947929036727-0.0887474513466-0.08875812920570.3183391805990.10120067208-0.201270463817-0.01522700933520.243267799466-4.55494552418E-60.512123200263-0.01646825171850.01055171459930.4665414699470.05417513957310.442043256004-18.493233458636.2456739127-25.7678395982
181.30469666628-0.860749216903-0.7767413663243.932387811310.8088323939131.584747998590.007699710188730.0246873471203-0.1445671697980.4329474810520.202722391681-0.4439945121250.04672182167420.3720538714133.71110924527E-50.482447287038-0.00278039121165-0.07165396881530.5235752407230.00154189965090.57953066575-17.162156238920.6115942147-29.7578634727
190.7488498807270.0729716836844-0.05437360511280.386135770542-0.4528293046861.059394673050.0629013207868-0.1214741458880.401478970416-0.0734325322944-0.1501500060490.169575433539-0.224610873613-0.3362675063332.30105454068E-50.504526009175-0.01282504152910.05116038562980.60059314197-0.1449795423330.620197314764-52.229533218410.8898443733-47.7208829997
200.3130430972610.471123175082-0.348415941891.0901149838-0.06344885316790.565985840785-0.115264385148-0.6600754023440.5120642577380.566261371963-0.05013227212310.1201782884190.140390926172-0.675863309875-0.0029803737340.698792702728-0.1111955029560.1523365519121.18223538861-0.232620670430.593523684731-60.15492749950.24829383537-33.3486717425
210.66519494885-0.649823848118-0.1703003924141.225003468740.2636079840440.792401534865-0.187660337368-0.479540225692-0.1601616137860.398807603401-0.05220692006070.1987597572510.714692764609-0.12128426285-0.004262369051940.755992647095-0.1592268426090.1222026409510.7860790051710.09020108884110.440858650935-56.2289855721-16.4183006759-41.4083148925
220.59986554843-0.5499070619750.3977078756250.448924159611-0.138505014230.289496962305-0.195388452441-0.0292955290405-0.234149486338-0.255364428249-0.0028524300268-0.03986044397730.488365795061-0.18751626006-3.0936720507E-50.746437366711-0.1470002998880.1092922664720.5019148553240.1019978797250.606580026337-51.687853155-20.7711543298-57.4783918897
230.4503618115910.5894654722910.3546097541331.624250380290.4238279041161.66106913359-0.1088504055040.03695660147010.216053528858-0.278188320459-0.003174001330490.1297125151680.229826599007-0.230571638781-1.02607994463E-50.455493822723-0.06760803849840.0177062622870.502926959320.01939601274340.485195317016-53.3411996774-5.28340051333-60.0546670797
240.5300728360220.655875700170.307603010680.6238441240810.590329802681-0.168683303192-0.2547789055640.2608238528390.359007897455-0.3015031375020.112886473550.130569072079-0.185915694958-0.0594488653263-0.0001194144548340.599679947066-0.02345815526450.01034152907810.5420513323710.02747597635890.569807724145-42.26775705827.08061958435-61.8221090787
251.247071808531.626212552820.5662152841032.04336492171.189387072961.98807422997-0.1929222268960.00619266278059-0.229085372395-0.140883926310.359825478767-0.4536075653240.1002066715650.2110512899177.75449348532E-50.499631875570.006330383999090.117574107590.481970401889-0.01832426409880.585576619049-26.7939515826-2.17141734768-56.4292828981
261.475071722270.5832783216550.7413354286612.344232892951.508241355842.436475164180.199721980387-0.0923261225453-0.4418063035730.4990338121660.330238727135-0.5230169464910.7870030310360.398685621001-7.6259295575E-50.6138385535250.078639317122-0.04279196093450.543250807674-0.04784734027910.753907516115-17.9273137128-0.607812315877-41.8568814408
270.5362353230770.04052305530630.7483962742571.625237961870.6420083271511.28387054613-0.0642307219108-0.136522312134-0.0527624848167-0.0555143733110.2181936283310.00815228164659-0.3151668155610.159581936518-6.65471391451E-50.426504418996-0.03837666027220.06780106670210.536167644623-0.003591889072450.56157879599-23.781165033113.8874930474-43.9286053446
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 5 through 42 )AA5 - 421 - 38
22chain 'A' and (resid 43 through 142 )AA43 - 14239 - 138
33chain 'A' and (resid 143 through 223 )AA143 - 223139 - 219
44chain 'A' and (resid 224 through 353 )AA224 - 353220 - 349
55chain 'A' and (resid 354 through 521 )AA354 - 521350 - 517
66chain 'A' and (resid 522 through 581 )AA522 - 581518 - 577
77chain 'B' and (resid 6 through 58 )BB6 - 581 - 53
88chain 'B' and (resid 59 through 142 )BB59 - 14254 - 135
99chain 'B' and (resid 143 through 253 )BB143 - 253136 - 246
1010chain 'B' and (resid 254 through 339 )BB254 - 339247 - 332
1111chain 'B' and (resid 340 through 432 )BB340 - 432333 - 425
1212chain 'B' and (resid 433 through 528 )BB433 - 528426 - 519
1313chain 'B' and (resid 529 through 580 )BB529 - 580520 - 569
1414chain 'C' and (resid 5 through 42 )CC5 - 421 - 38
1515chain 'C' and (resid 43 through 223 )CC43 - 22339 - 210
1616chain 'C' and (resid 224 through 323 )CC224 - 323211 - 310
1717chain 'C' and (resid 324 through 493 )CC324 - 493311 - 480
1818chain 'C' and (resid 494 through 581 )CC494 - 581481 - 565
1919chain 'D' and (resid 6 through 82 )DD6 - 821 - 76
2020chain 'D' and (resid 83 through 142 )DD83 - 14277 - 136
2121chain 'D' and (resid 143 through 213 )DD143 - 213137 - 207
2222chain 'D' and (resid 214 through 246 )DD214 - 246208 - 240
2323chain 'D' and (resid 247 through 299 )DD247 - 299241 - 293
2424chain 'D' and (resid 300 through 339 )DD300 - 339294 - 333
2525chain 'D' and (resid 340 through 432 )DD340 - 432334 - 426
2626chain 'D' and (resid 433 through 541 )DD433 - 541427 - 534
2727chain 'D' and (resid 542 through 580 )DD542 - 580535 - 571

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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