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- PDB-6orr: Co-crystal structure of human NicotinamideN-Methyltransferase (NN... -

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基本情報

登録情報
データベース: PDB / ID: 6orr
タイトルCo-crystal structure of human NicotinamideN-Methyltransferase (NNMT) in complex with High-Affinity Alkynyl Bisubstrate Inhibitor NS1
要素NNMT protein
キーワードTRANSFERASE/TRANSFERASE INHIBITOR / methyltransferase nicotinamide / alkynyl bisubstrate inhibitor / alkyne linker methyltransferase inhibitor / high-affinity alkynyl nucleoside / SAM slow-binding inhibition / tight-binding inhibition / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
機能・相同性
機能・相同性情報


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / positive regulation of protein deacetylation / Metabolism of ingested SeMet, Sec, MeSec into H2Se / Methylation / : / positive regulation of gluconeogenesis / methylation / cytosol
類似検索 - 分子機能
Methyltransferase, NNMT/PNMT/TEMT / Methyltransferase NNMT/PNMT/TEMT, conserved site / : / NNMT/PNMT/TEMT family / NNMT/PNMT/TEMT family of methyltransferases signature. / SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-N37 / Nicotinamide N-methyltransferase / NNMT protein
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: 2.25 Å
データ登録者May, E.J. / Policarpo, R.L. / Gaudet, R.
資金援助 米国, 4件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 米国
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 米国
National Science Foundation (NSF, United States)DGE1144152. 米国
Department of Energy (DOE, United States)DE-AC02-06CH11357 米国
引用
ジャーナル: J.Med.Chem. / 年: 2019
タイトル: High-Affinity Alkynyl Bisubstrate Inhibitors of NicotinamideN-Methyltransferase (NNMT).
著者: Policarpo, R.L. / Decultot, L. / May, E. / Kuzmic, P. / Carlson, S. / Huang, D. / Chu, V. / Wright, B.A. / Dhakshinamoorthy, S. / Kannt, A. / Rani, S. / Dittakavi, S. / Panarese, J.D. / Gaudet, R. / Shair, M.D.
#1: ジャーナル: ChemRxiv / 年: 2019
タイトル: High-Affinity Alkynyl Bisubstrate Inhibitors of NicotinamideN-Methyltransferase (NNMT)
著者: Policarpo, R.L. / Decultot, L. / May, E.J. / Kuzmic, P. / Carlson, S. / Huang, D. / Chu, V. / Wright, B. / Dhakshinamoorthy, S. / Kannt, A. / Rani, S. / Dittakavi, S. / Panarese, J.D. / Gaudet, R. / Shair, M.D.
履歴
登録2019年4月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年10月23日Provider: repository / タイプ: Initial release
改定 1.12019年11月27日Group: Author supporting evidence / Database references / カテゴリ: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_audit_support.funding_organization
改定 1.22023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: NNMT protein
B: NNMT protein
C: NNMT protein
D: NNMT protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)128,36313
ポリマ－125,8644
非ポリマー2,4999
水3,225179
1
A: NNMT protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,3446
ポリマ－31,4661
非ポリマー8785
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: NNMT protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,9762
ポリマ－31,4661
非ポリマー5101
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: NNMT protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,0683
ポリマ－31,4661
非ポリマー6022
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: NNMT protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)31,9762
ポリマ－31,4661
非ポリマー5101
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
A: NNMT protein
D: NNMT protein
ヘテロ分子

B: NNMT protein
C: NNMT protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)128,36313
ポリマ－125,8644
非ポリマー2,4999
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area6230 Å2
ΔGint-33 kcal/mol
Surface area39020 Å2
手法PISA
単位格子
Length a, b, c (Å)46.074, 62.203, 108.202
Angle α, β, γ (deg.)82.519, 81.844, 68.353
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
11(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...
21(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...
31(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEPHEPHE(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA524
12ASPASPASPASP(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA1938
13TYRTYRTYRTYR(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA2443
14SERSERSERSER(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA3251
15SERSERSERSER(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA3554
16GLYGLYGLYGLY(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA5675
17GLUGLUGLUGLU(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA8099
18ASNASNASNASN(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA90109
19GLUGLUGLUGLU(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA95114
110VALVALVALVAL(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA122141
111ALAALAALAALA(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA134153
112ASPASPASPASP(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA142161
113ARGARGARGARG(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA178197
114GLNGLNGLNGLN(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA209228
115GLUGLUGLUGLU(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA219238
116LYSLYSLYSLYS(CHAIN A AND (RESID 5 THROUGH 17 OR RESID 19...AA259278
21PHEPHEPHEPHE(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB524
22ASPASPASPASP(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB1938
23TYRTYRTYRTYR(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB2443
24SERSERSERSER(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB3251
25SERSERSERSER(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB3554
26GLYGLYGLYGLY(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB5675
27GLUGLUGLUGLU(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB8099
28ASNASNASNASN(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB90109
29GLUGLUGLUGLU(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB95114
210VALVALVALVAL(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB122141
211ALAALAALAALA(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB134153
212ASPASPASPASP(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB142161
213ARGARGARGARG(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB178197
214GLNGLNGLNGLN(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB209228
215GLUGLUGLUGLU(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB219238
216LYSLYSLYSLYS(CHAIN B AND (RESID 5 THROUGH 17 OR RESID 19...BB259278
31PHEPHEPHEPHE(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD524
32ASPASPASPASP(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD1938
33TYRTYRTYRTYR(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD2443
34SERSERSERSER(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD3251
35SERSERSERSER(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD3554
36GLYGLYGLYGLY(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD5675
37GLUGLUGLUGLU(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD8099
38ASNASNASNASN(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD90109
39GLUGLUGLUGLU(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD95114
310VALVALVALVAL(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD122141
311ALAALAALAALA(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD134153
312ASPASPASPASP(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD142161
313ARGARGARGARG(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD178197
314GLNGLNGLNGLN(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD209228
315GLUGLUGLUGLU(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD219238
316LYSLYSLYSLYS(CHAIN D AND (RESID 5 THROUGH 17 OR RESID 19...DD259278

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要素

#1: タンパク質
NNMT protein / Nicotinamide N-methyltransferase / isoform CRA_a


分子量: 31466.033 Da / 分子数: 4 / 変異: K100A, E101A, E103A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NNMT, hCG_39357 / プラスミド: pET28a-LIC / 詳細 (発現宿主): N-terminal hexaHis tag / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q6FH49, UniProt: P40261*PLUS
#2: 化合物
ChemComp-N37 / 9-{9-amino-6-[(3-carbamoylphenyl)ethynyl]-5,6,7,8,9-pentadeoxy-D-glycero-alpha-L-talo-decofuranuronosyl}-9H-purin-6-amine


分子量: 509.514 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C24H27N7O6 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C3H8O3
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 179 / 由来タイプ: 天然 / 式: H2O

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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: 2.43 Å3/Da / 溶媒含有率: 49.44 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / pH: 6.8 / 詳細: 100 mM HEPES pH 6.8, 2 M ammonium sulfate

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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-C / 波長: 0.9791 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2018年11月10日
放射モノクロメーター: Cryo-Cooled double crystal / 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: 0.9791 Å / 相対比: 1
反射解像度: 2.25→42.6 Å / Num. obs: 46037 / % possible obs: 87.23 % / 冗長度: 1.8 % / Biso Wilson estimate: 28.86 Å2 / CC1/2: 0.919 / Rmerge(I) obs: 0.1752 / Rpim(I) all: 0.1752 / Rrim(I) all: 0.2478 / Net I/σ(I): 3.15
反射 シェル解像度: 2.25→2.33 Å / 冗長度: 1.8 % / Rmerge(I) obs: 1.151 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 4664 / CC1/2: 0.182 / Rpim(I) all: 1.151 / Rrim(I) all: 1.628 / % possible all: 86.28

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
Aimless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
開始モデル: 3ROD

3rod


解像度: 2.25→42.6 Å / SU ML: 0.3213 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 28.5379
Rfactor反射数%反射Selection details
Rfree0.2631 2294 5.02 %Random selection
Rwork0.2221 ---
obs0.2241 45706 87.22 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 36.33 Å2
精密化ステップサイクル: LAST / 解像度: 2.25→42.6 Å
タンパク質核酸リガンド溶媒全体
原子数8212 0 178 179 8569
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00198614
X-RAY DIFFRACTIONf_angle_d0.49211686
X-RAY DIFFRACTIONf_chiral_restr0.04041312
X-RAY DIFFRACTIONf_plane_restr0.00381472
X-RAY DIFFRACTIONf_dihedral_angle_d10.57025137
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.34441410.31832763X-RAY DIFFRACTION86.38
2.3-2.350.30961470.28262560X-RAY DIFFRACTION85.05
2.35-2.410.30231340.26462683X-RAY DIFFRACTION84.87
2.41-2.470.32921340.26462457X-RAY DIFFRACTION79.11
2.47-2.550.29511200.26942516X-RAY DIFFRACTION81.71
2.55-2.630.31311570.26062883X-RAY DIFFRACTION92.04
2.63-2.720.3121530.25742874X-RAY DIFFRACTION91.59
2.72-2.830.29921400.24542801X-RAY DIFFRACTION90.52
2.83-2.960.29981490.24482754X-RAY DIFFRACTION89.24
2.96-3.120.2611490.23662722X-RAY DIFFRACTION86.61
3.12-3.310.28411220.2352475X-RAY DIFFRACTION79.88
3.31-3.570.22841440.20992913X-RAY DIFFRACTION93.51
3.57-3.930.22121590.18632846X-RAY DIFFRACTION91.95
3.93-4.50.23471420.17292772X-RAY DIFFRACTION88.54
4.5-5.660.23661580.18962674X-RAY DIFFRACTION86.32
5.66-490.23961450.21232719X-RAY DIFFRACTION88.12
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)
13.047957716920.64755261717-1.403460150773.47713066762-1.791314586791.22224858831-0.5014533299690.729761186887-0.620812469405-0.713196600540.544852612726-0.09650464884720.898390725571-0.140575599458-0.07780753961660.5043327828680.09016731157510.1156457639030.210553817313-0.0989001426310.2492803826063.88088797022-3.48838887624-19.9850014572
25.665385583145.747164857045.366338824095.822255751545.54603075697.131771013770.9203817989980.316672609197-1.091882428850.4100243406020.0954279676881-1.257359031781.291243429911.14434993553-0.009693746791380.3406751638490.1530569633590.04412486576380.382762179707-0.03119259075660.30711201107113.2053954313-8.32741428398-1.10280276953
32.232812725850.2061588059860.4732295675452.23873828304-0.1391180398292.949449762720.14578527697-0.173986971115-0.2388500391260.334126150147-0.0726894815176-0.1093725548190.2437635942050.00738365431014-0.02990051698310.2625811610820.03078877634740.05305737015710.1677602702450.02406935921010.195527378288-1.30835291131-7.175858020825.85055634118
42.246315104120.996681421102-0.5604958446672.06419391750.1510070778142.083182432930.07104715000080.1214535563950.16649954094-0.07069518052390.01510751545060.106719745053-0.107244639715-0.067880689577-0.1123851452770.1871437266140.07009330846830.06772067790590.1581719111240.052413570450.19846759408-3.720484863833.87823325233-5.63095904214
55.92738323343-1.02386112240.7346906587762.6790819668-0.6660535411282.705363344610.4021908247280.1293548566040.179848862802-0.283211037536-0.0916947810704-0.018415678012-0.502702639888-0.0337949005468-0.07276176867630.2964595279280.04415740731140.07948687442730.1356270657940.03358050599460.2219899648671.5379893745611.0319772396-0.263836782856
61.80901415601-1.066484482711.766655557031.31550139350.7448357040416.976038609070.191160869503-0.4596230109140.1058132528551.15259046991-0.3099228712670.737976253683-0.473217984622-0.06691326238390.08000186364410.547630203998-0.0158012995970.2054106783020.327993520246-0.1000789383510.38530246155425.2899116113-27.078156164628.1143442989
76.50986850267-1.38038656417-0.3121783600453.108579738390.1532730644772.286749758580.1533933185850.4404616563650.390678950796-0.344554761306-0.08529140339650.2451747593620.210441039299-0.139061671967-0.1092368306070.490780783569-0.04088351761540.0312257553650.242423520070.0344228371420.27837189280626.0937572339-43.696242285220.0200975381
83.444694936951.640800510780.3658870790871.14124601812-0.7784336036982.340479856670.328896293635-0.0197473925397-0.5217004425480.2793955931130.030516986484-0.2993404274760.453633428969-0.0740209852324-0.1979844492350.5155023691140.0476152861558-0.1309763086880.2600987456110.05682175172880.30952967847339.0914232896-41.562628145322.5451961958
92.381177728612.12872572126-0.4374183522052.8434416030.6890298803952.520773074950.248597371096-0.351983085026-0.5557613024490.767979291753-0.407896370342-0.4810957120160.1498718686270.4225253678710.1493876853440.5716646261090.00978155685905-0.0616329333510.2936344701180.05920790192420.2033207219438.9827036547-39.457676402926.4343514045
102.6918630208-0.285135028765-0.1570353997620.831083453384-0.7346713492151.89144262788-0.0927464335151-0.945000854960.1464836695430.725071008062-0.3125140086510.1886991591490.0667147253108-0.1972006736770.1276845039270.847832776998-0.05768404897140.01369325801110.3529161948780.0940529924960.013791045763235.388858605-38.856189206331.9383419834
113.857809198770.5547444009120.6758294434312.642728938620.1738596525292.65366645318-0.0889266435156-0.144270577155-0.0865668475565-0.0027598653193-0.0503623016781-0.31685140554-0.1410054642390.09285505869720.1831086346850.3131054269850.02003846351360.03066535410670.1398674934860.02271625706990.14392193080540.9536514083-31.759044361315.2045160106
123.635438531150.562562948253-0.18944990042.94183992477-0.09749668877631.77625214978-0.08851926735260.363130585267-0.0118432603034-0.172720135568-0.1342594010410.447470920878-0.507888653172-0.2337996092890.09390116807190.306060633250.0775858437317-0.003965158004090.138263610060.04050922845410.16351131653529.3379190927-30.569918833311.2905588548
134.687156652071.567102644530.4913586839312.39424022069-0.274463055982.118219308870.517449217227-0.08866984984470.0121146026999-0.159151919414-0.3174361718750.266968120396-0.112229481337-0.176225268324-0.1660623212960.310112931410.04580454249790.0198711130810.185353240906-0.05830041604260.12829880727227.0439030169-34.662646381613.2558152459
143.05240276919-2.198828601510.8962942565135.98175033783-3.554254386796.12870681396-0.308963571107-0.6820034101360.2978747937870.488865225560.239882673442-0.0263294394723-0.844208192741-0.3701023725160.03187705884650.3851550611190.03166755799620.003159229673880.278204018141-0.06604935235460.17623420576427.1200868225-20.3100207273-3.92433998826
157.94860009076-1.26550342507-0.5074158814247.048085001972.133214928116.375771699351.042279613620.1876105381120.3735388235810.243006699977-0.190258626584-1.07051083129-0.8360826760360.831939713151-0.04728132952110.294162862731-0.042945203473-0.06598229294160.2692940728010.1702393928390.28527119162335.1605353689-15.3106188793-22.7276928636
164.354602104750.7797139179141.521576158233.247261129182.058792762963.446494690610.42587571097-0.119600766864-0.702219301996-0.3746570975320.485588404213-0.518641473510.2830711643690.6858792121690.0004062908224180.2388101123420.2237906373770.04161671002830.1913346830950.07259339677380.15118951592730.2117729185-25.4804478306-32.138992377
171.997778783520.738179480479-0.7433887520132.769389311090.10968809476.107349553950.08252288834680.392834917826-0.155168648117-0.2276747986450.124496703214-0.1393058906640.18920896653-0.416939375651-0.2097017896110.2176067011310.1043096443830.0007155344900940.2082059348770.01860098398090.22579157761917.4377967248-19.6348262338-30.1048731813
181.71661951758-0.213480155070.05802347394842.04241132126-0.1306806542482.113384228870.1517206876160.1448077571780.393012506706-0.202827868544-0.116474706184-0.0746534295664-0.553054019411-0.0958046486017-0.0688523284440.3105799716090.1247722020360.01771657141910.1953169098160.03753538564040.2241949685821.5246232027-12.5034467946-28.8011038407
193.04426587265-0.247853626040.282164510782.156303574520.3855287511031.797412246710.166845000829-0.147768756469-0.1414155850650.184147255193-0.1541496318710.03398654575940.189105608774-0.102589442598-0.04519417132850.2262568209310.0337992878522-0.006343202873490.1084518047740.05002075261190.16068940678819.2710567567-27.7500739129-18.1531454051
201.90190550034-0.396205120159-0.4010999800081.5784042379-0.5187696179352.777092613360.395979153463-0.00407351066725-0.07325493643320.1156428359360.158778874220.04100426510791.10244146573-0.372109848575-0.1466244456980.4231196101120.0402050571318-0.2112512651940.07778207509490.178841104130.40422969142120.3466944575-38.3488928384-25.0157707233
215.3174647265-0.5055571676223.052593463463.60844142581.098625380725.322449957360.186159826409-0.602793379568-0.01165620358360.306956350905-0.0869523066809-0.2408876663940.4165697551660.0110367160529-0.1381335585630.2569399602660.0452918930960.05009575220940.142771043740.02145332206280.23030975767227.3232055406-31.5240451048-22.7411829689
225.296210015550.520814907526-2.209194312821.961507744381.123857089936.400691836610.3115724653970.825791241959-0.028308133246-0.855072416296-0.3688172462880.2727964972420.171007235354-0.01882349760790.08133223107480.5544871391580.0708640671379-0.1082541049050.323258901271-0.05334004718470.2490158815681.257038811923.31793376428-51.325599309
232.01633076217-0.5902215719720.1728954763431.91254489868-0.08694844776972.630778123920.09177590603720.3624444172240.237419234408-0.442384795387-0.136504682441-0.111098974997-0.2004591332520.1801739740420.1048023050080.4733663194310.1138092293440.0624397676610.2630688309440.06180910162380.21976181994913.016206507213.8909484922-48.4115353554
246.593238013591.100793591111.962788145373.584222772991.290654359943.03306290467-0.00842630159247-0.2434415987670.033630763079-0.0572715543079-0.08957937409340.2347391610140.157404658964-0.1672061458270.1319585545720.2529702322810.07159666389730.04484410918640.1648595225260.03057318920.1165632691155.118015740418.12455615222-35.74602209
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -10 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 150 )
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 260 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 32 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 49 )
8X-RAY DIFFRACTION8chain 'B' and (resid 50 through 68 )
9X-RAY DIFFRACTION9chain 'B' and (resid 69 through 87 )
10X-RAY DIFFRACTION10chain 'B' and (resid 88 through 150 )
11X-RAY DIFFRACTION11chain 'B' and (resid 151 through 198 )
12X-RAY DIFFRACTION12chain 'B' and (resid 199 through 238 )
13X-RAY DIFFRACTION13chain 'B' and (resid 239 through 261 )
14X-RAY DIFFRACTION14chain 'C' and (resid -10 through 16 )
15X-RAY DIFFRACTION15chain 'C' and (resid 17 through 32 )
16X-RAY DIFFRACTION16chain 'C' and (resid 33 through 49 )
17X-RAY DIFFRACTION17chain 'C' and (resid 50 through 87 )
18X-RAY DIFFRACTION18chain 'C' and (resid 88 through 150 )
19X-RAY DIFFRACTION19chain 'C' and (resid 151 through 217 )
20X-RAY DIFFRACTION20chain 'C' and (resid 218 through 238 )
21X-RAY DIFFRACTION21chain 'C' and (resid 239 through 262 )
22X-RAY DIFFRACTION22chain 'D' and (resid 5 through 32 )
23X-RAY DIFFRACTION23chain 'D' and (resid 33 through 198 )
24X-RAY DIFFRACTION24chain 'D' and (resid 199 through 261 )

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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