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- PDB-7qkd: Crystal structure of human Cathepsin L in complex with covalently... -

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基本情報

登録情報
データベース: PDB / ID: 7qkd
タイトルCrystal structure of human Cathepsin L in complex with covalently bound MG132
要素Cathepsin L
キーワードHYDROLASE / cathepsin / cystein protease / drug development / drug target / peptide-like inhibitor / lysosome / protein degradation / SARS-CoV-2 / COVID-19 / spike protein maturation
機能・相同性
機能・相同性情報


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / protein autoprocessing / Collagen degradation / fibronectin binding / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / endocytic vesicle lumen / Attachment and Entry / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / adaptive immune response / receptor-mediated endocytosis of virus by host cell / lysosome / Attachment and Entry / immune response / symbiont entry into host cell / apical plasma membrane / cysteine-type endopeptidase activity / fusion of virus membrane with host plasma membrane / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
類似検索 - 分子機能
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
類似検索 - ドメイン・相同性
PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form / ACETATE ION / Chem-ALD / DI(HYDROXYETHYL)ETHER / Procathepsin L
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.5 Å
データ登録者Reinke, P.Y.A. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Rahmani Mashhour, A. / Hauser, M. / Karnicar, K. / Usenik, A. / Lindic, N. ...Reinke, P.Y.A. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Rahmani Mashhour, A. / Hauser, M. / Karnicar, K. / Usenik, A. / Lindic, N. / Lach, M. / Boehler, H. / Beck, T. / Cox, R. / Chapman, H.N. / Hinrichs, W. / Turk, D. / Guenther, S. / Meents, A.
資金援助 ドイツ, スロベニア, 6件
組織認可番号国
Helmholtz AssociationFISCOV ドイツ
Helmholtz AssociationSFragX ドイツ
German Federal Ministry for Education and Research16GW0277 ドイツ
German Federal Ministry for Education and Research031B0405 ドイツ
Slovenian Research AgencyP1-0048 スロベニア
Slovenian Research AgencyIO-0048 スロベニア
引用ジャーナル: J.Med.Chem. / 年: 2024
タイトル: Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors.
著者: Falke, S. / Lieske, J. / Herrmann, A. / Loboda, J. / Karnicar, K. / Gunther, S. / Reinke, P.Y.A. / Ewert, W. / Usenik, A. / Lindic, N. / Sekirnik, A. / Dretnik, K. / Tsuge, H. / Turk, V. / ...著者: Falke, S. / Lieske, J. / Herrmann, A. / Loboda, J. / Karnicar, K. / Gunther, S. / Reinke, P.Y.A. / Ewert, W. / Usenik, A. / Lindic, N. / Sekirnik, A. / Dretnik, K. / Tsuge, H. / Turk, V. / Chapman, H.N. / Hinrichs, W. / Ebert, G. / Turk, D. / Meents, A.
履歴
登録2021年12月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年12月28日Provider: repository / タイプ: Initial release
改定 1.12024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年5月15日Group: Author supporting evidence / Database references
カテゴリ: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_audit_support.country

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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: Cathepsin L
B: Cathepsin L
C: Cathepsin L
D: Cathepsin L
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)99,35916
ポリマ－96,6474
非ポリマー2,71212
水16,790932
1
A: Cathepsin L
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,8524
ポリマ－24,1621
非ポリマー6903
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Cathepsin L
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,7453
ポリマ－24,1621
非ポリマー5842
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Cathepsin L
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,7453
ポリマ－24,1621
非ポリマー5842
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Cathepsin L
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,0176
ポリマ－24,1621
非ポリマー8555
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)57.280, 62.710, 68.070
Angle α, β, γ (deg.)105.536, 93.388, 115.360
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

#1: タンパク質
Cathepsin L


分子量: 24161.676 Da / 分子数: 4 / 変異: T110A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CTSL, CTSL1 / 発現宿主: Komagataella phaffii GS115 (菌類) / 参照: UniProt: P07711
#2: 化合物
ChemComp-ALD / N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide


タイプ: Peptide-like / クラス: 阻害剤 / 分子量: 477.637 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C26H43N3O5 / タイプ: SUBJECT OF INVESTIGATION / 参照: PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form
#3: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C4H10O3
#4: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H3O2
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 932 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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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: 2.16 Å3/Da / 溶媒含有率: 43.01 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 4
詳細: Mature cathepsin L at a concentration of 7 mg/ml was equilibrated against 27% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0. Crystals, which grew at 293 K to final size after ...詳細: Mature cathepsin L at a concentration of 7 mg/ml was equilibrated against 27% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0. Crystals, which grew at 293 K to final size after approximately 3 days, were transferred to a compound soaking solution containing 22% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0 as well as 5% v/v DMSO and 10% v/v PEG 400.

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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, DESY / ビームライン: P11 / 波長: 1.033 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2021年8月14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: 1.033 Å / 相対比: 1
反射解像度: 1.5→44.35 Å / Num. obs: 118682 / % possible obs: 91.57 % / 冗長度: 10.8 % / Biso Wilson estimate: 16.02 Å2 / CC1/2: 0.982 / CC star: 0.995 / Rpim(I) all: 0.08 / Rrim(I) all: 0.2597 / Net I/σ(I): 8.94
反射 シェル解像度: 1.5→1.554 Å / Mean I/σ(I) obs: 1.93 / Num. unique obs: 10402 / CC1/2: 0.762 / CC star: 0.93 / Rpim(I) all: 0.3829 / Rrim(I) all: 1.275 / % possible all: 79.93

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13-2998_9999精密化
XDSデータ削減
XSCALEデータスケーリング
PHENIX1.13-2998_9999位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3OF9

3of9


解像度: 1.5→44.35 Å / SU ML: 0.1825 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 23.2264 / 立体化学のターゲット値: GeoStd + Monomer Library
Rfactor反射数%反射
Rfree0.1983 3488 1.49 %
Rwork0.1798 230090 -
obs0.1801 118538 90.22 %
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: 25.75 Å2
精密化ステップサイクル: LAST / 解像度: 1.5→44.35 Å
タンパク質核酸リガンド溶媒全体
原子数6750 0 189 932 7871
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00647362
X-RAY DIFFRACTIONf_angle_d0.82129963
X-RAY DIFFRACTIONf_chiral_restr0.0518973
X-RAY DIFFRACTIONf_plane_restr0.00551358
X-RAY DIFFRACTIONf_dihedral_angle_d16.14714382
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.30051070.28576794X-RAY DIFFRACTION66.41
1.52-1.540.29551420.28168298X-RAY DIFFRACTION81.67
1.54-1.570.30781120.27219017X-RAY DIFFRACTION88.44
1.57-1.590.29151470.25639255X-RAY DIFFRACTION90.26
1.59-1.620.26141480.24959288X-RAY DIFFRACTION91.29
1.62-1.640.2541410.24689454X-RAY DIFFRACTION92.65
1.64-1.670.29541360.24389352X-RAY DIFFRACTION92.51
1.67-1.710.29551520.22989463X-RAY DIFFRACTION92.36
1.71-1.740.25791290.21529490X-RAY DIFFRACTION91.87
1.74-1.780.20961660.2119212X-RAY DIFFRACTION91.58
1.78-1.820.2551410.20689245X-RAY DIFFRACTION90.76
1.82-1.870.20011180.19068871X-RAY DIFFRACTION87.09
1.87-1.920.21091320.19318799X-RAY DIFFRACTION85.84
1.92-1.970.19581400.18729682X-RAY DIFFRACTION94.57
1.97-2.040.21371520.17769618X-RAY DIFFRACTION94.41
2.04-2.110.21361410.17639582X-RAY DIFFRACTION94
2.11-2.190.21921440.17369608X-RAY DIFFRACTION93.99
2.19-2.290.20491440.17199491X-RAY DIFFRACTION93.07
2.29-2.410.22031480.16819438X-RAY DIFFRACTION92.48
2.41-2.560.1811370.16779091X-RAY DIFFRACTION89.4
2.56-2.760.17411390.1638776X-RAY DIFFRACTION86.09
2.76-3.040.14251410.16749768X-RAY DIFFRACTION95.39
3.04-3.480.17781330.16159727X-RAY DIFFRACTION95.27
3.48-4.380.15861480.14919492X-RAY DIFFRACTION93.16
4.38-44.350.17581500.16919279X-RAY DIFFRACTION91.1
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)
17.165110063911.99416049551.399585928513.711575692710.6887295436832.06927272715-0.0731105121925-0.264381233650.196992756157-0.0222342210447-0.0226478213256-0.082240110006-0.130060547244-0.08263664340930.07278463984710.1402530346970.02285368327730.0245677624280.106128098417-0.04198976888150.075420331230126.0201476722-9.0463645579-5.91140353924
23.890246511832.05188511748-1.322017458823.02367437905-1.348002710543.97830150824-0.05398603334740.239957576491-0.191301043476-0.1236755638250.0865273575737-0.347118790125-0.1135677037260.1684981016240.003611067887220.129552311759-0.01487681742630.01269755519670.154686785839-0.06351284598670.12728838653626.2455574536-16.3735605775-12.3651033213
32.731823809240.8843532165541.409721973492.789288700781.169675574611.01361465256-0.09142952123750.1203792711390.00763796936037-0.2873414475940.0984361499183-0.161004020994-0.0762245334135-0.0262960319297-0.01247334406490.12567586755-0.01466244997620.03631039364440.138444868172-0.02676797196130.099867326154819.3174601569-18.9057092741-16.4118155668
42.541014234250.1364861584170.5024812212013.422651941830.1574758872654.49973327696-0.002002402781340.135232590466-0.141130000106-0.1412582586560.05056681082-0.001858197910960.0370642282763-0.249729046945-0.04432838932640.116564246798-0.05059592741440.007379324486530.143698620501-0.0437418053780.12920203054716.0031132361-22.8470539659-16.0008183579
51.400211161860.7972053746220.791804329451.70441591960.364998180374.072252266230.2114129999180.0414880417636-0.5463869976930.1168537100770.223615334397-0.5571765297660.3667437509230.0504563919675-0.389077923660.1512484348650.0202604986864-0.04027630507740.122439525712-0.03842180552070.32214098029533.0576758105-21.4151133471-3.8701711074
60.6293615379810.3616835249191.297190545640.9468754330071.345303666442.680330708310.113342223842-0.280608444029-0.01585926823860.161358459252-0.1487206724080.02329835650170.162133969221-0.6744781665160.007335378745930.135459144653-0.0272192381627-0.0006439987284130.2691421178440.001247619177280.15652098651824.0055279749-11.09644289077.31459800813
73.1527684508-0.1777994335560.8900921264362.448131882771.543816562893.29171492010.114396310809-0.3090425255410.0397538318920.100891906186-0.121695132107-0.1422182073830.0765273742189-0.291502426604-0.004871217518510.100992414383-0.044345972560.002078900337240.14261441859-0.01628170652980.14020123566524.4244705141-12.45957585762.3242553032
82.438470669630.4623943652930.03910494766042.83220299461-0.3404060874662.722724393360.01500223827070.1060925533930.0812104887722-0.05481241624860.01113504375760.0447547187489-0.214363394552-0.00800789357336-0.006821317224360.06438155764570.007800880927550.01219183784530.114987749392-0.01134956390940.094035911452355.68104553027.2494286291416.4541878994
92.63690306925-0.850551743564-0.814532293868.486673145813.795639964823.637132468110.0670885185965-0.136377431213-0.0259779018134-0.0155249751702-0.04710235773040.0943648228238-0.09641368208450.0205582318659-0.0123779739230.08506848419670.00776398363625-0.006684240727520.09483007420340.01791188640050.085710832244949.08414192562.4017160850723.006226303
102.091060604251.287882627030.6917718487682.18280175421-0.2259462620091.085097020590.0660203359722-0.0844648607344-0.2455800449060.04262551261960.0223650469402-0.0586641685150.1375774256250.0440212825016-0.0999876883720.09315054285370.0205292115301-0.007144652583830.09364820796950.01389582348730.14044976169247.2726268247-7.7167113740623.569707316
115.268962110190.199459373054-2.905945417042.04574371753-0.4011800632914.22001048564-0.0137957530644-0.225201646116-0.3082813914080.231172251532-0.158432615509-0.261553862540.2075823866330.1359421250970.1719182792570.1354413645550.0017629975375-0.06114246626330.12938503880.06432509281570.16477985408453.380603988-9.6780162623131.5668848607
122.334350432090.417477413330.1555265517071.63793099392-1.698439046144.21781352617-0.007150509279970.2907593042790.138464418271-0.07746394141480.1898343934180.106227829454-0.0748660695986-0.271277909027-0.1872094585380.08831771924880.0359103649573-0.00605377476420.10996441530.002526302011680.13096474711941.81464250065.6091710184913.4689083962
131.853596560320.099386973248-1.713088718271.264435033241.067662094822.73816611445-0.1450778244220.122373115836-0.161495851616-0.1567724571810.137602296225-0.163276573285-0.02268960785360.0913959811601-0.01989808152560.1374620108680.0106560076070.005236306844490.169175059725-0.01870283063380.15381095057457.95077614070.2506289745384.23032860895
142.505962699180.2773971026070.2756736348194.86782404510.417311979673.14303420813-0.004873020609360.5165786403740.114854236326-0.3079534023160.01039656424210.141346235714-0.1825826118540.0196038144255-0.01050363960180.08528738417630.01706017167110.01691701041760.2005146989650.02085231163550.12315616860353.28182049757.359146606254.01961106363
155.886980979960.991899297535-1.730522528992.00059714334-2.19002830187.585297121220.09337684307060.0805093922489-0.06639004861610.107850131729-0.0454154882149-0.0950613902283-0.2796548278230.610936256877-0.06278793764250.1182641471020.004933970570080.00679619341010.165189792085-0.03040300896810.16371362509864.87214274330.0042851188878612.8442957082
166.98665430159-1.11186447532.733387155962.69119172116-2.779338353123.24599327913-0.1750585182220.5212877269110.185910940414-0.131914884630.0486729905651-0.0491051238218-0.1009216160360.1330508037170.03693819458770.1496181538310.01499285649070.04668710235380.146506466528-0.0163755721490.12213013186753.73551668966.327039090042.39406797427
171.938155155720.270256568825-2.23000853261.457107245320.5762474376148.893357334280.06629459180760.183318555040.124726653958-0.08568479107270.0425170998006-0.0483574028119-0.1547538464090.0230997549408-0.08359524534610.1274960187870.0134203631506-0.005177112414440.1387905943790.01059864814030.15461760195944.86590712262.0711522657411.1240511475
182.86733259191.50140133394-0.3235121487952.01114487121-0.5766737492751.7243622224-0.06310751645810.165489469651-0.0833630957167-0.03358723904220.0319008537041-0.0716066847320.1045552828080.03108916633470.04289529413730.126264849499-0.002901336142340.003646024541640.135598696449-0.0005704651163330.097089413407630.912331248412.08978575-15.2755364391
195.401269432920.660448322911-2.50577167354.35627920242-0.5467500426446.85377542274-0.0715687364266-0.157113803408-0.4159377643660.178257178308-0.0619278552815-0.3448254748870.1837446433450.3077155762080.150045036780.1085734879510.00221445790016-0.02243760904890.2024300958780.0301162630430.21302071480143.99837327711.9915184464-12.0762604423
205.42983598253-0.37031522018-0.07752315984461.60689180321-0.6452572698412.18366330256-0.2968645608390.5540343922330.302294853593-0.01467101763770.2500279801170.1474803366430.027100777966-0.3341602516590.008756583730160.215880392879-0.028064450637-0.01973945059070.2880111863870.03623275892870.14506209181320.633401564615.1464086978-23.1310026693
211.66896597784-0.0604692618532-1.68710877211.272006846540.233337243673.443972546270.1569527942480.04816053673080.152245552990.131661674478-0.03073849583910.100170038261-0.0998372772329-0.336095983417-0.1191655328630.174957452624-0.03148470207830.01077451643390.205285834330.01484519652720.18735963761718.904339764716.5828075007-7.33169333266
221.88403598417-0.2160922073640.7584004152381.309771634550.8538618761341.027530122140.1672547136290.1124194448140.1780958564930.126720240856-0.1784242136040.148940828425-0.00568239440712-0.421687073990.0218528985780.235380096436-0.05878177779440.05673853309070.329510166373-0.008954566850140.2092368447311.715692047711.9681491619-0.434506414749
234.461716294760.306521552329-0.0374841859593.409897170750.4925906145942.63889210917-0.02293319171410.06086536320680.07119245589410.177246516447-0.01768488738740.483841233481-0.0149267002952-0.5140634666980.03005635544630.160606925415-0.01216904715250.04578468036570.2618849619030.02540500218630.16411478803913.419865963713.6894642092-10.677865094
244.716426444441.27669483274-0.944182431784.55372947571-0.04337668343512.036433429170.00150080882822-0.199319173819-0.4943793167570.04516795372090.01494298557960.3047840305190.260242424448-0.5764121658830.03615925244490.251876353737-0.07160450661790.03161609468250.2701849190030.02048493544230.19607810973122.24572108557.36323923505-1.57017041452
255.25031054693-0.8260092809271.153504462372.45162885182-1.792212456443.165055132570.06517454353510.0493771729552-0.207916432923-0.1768487734360.1360393545370.4473077932470.144690711268-0.54233697751-0.1355349799120.177040600283-0.05147630127840.03480387081560.309446624343-0.02355662839840.18661998917210.763279442213.710552407-9.92327965077
265.47337479709-1.22530662919-3.472883572563.177518731010.9993752179456.569731244040.09362346741410.08647851883520.199461319738-0.1270658436780.02730051397490.08564012124450.129002625268-0.237489615672-0.07862356201380.196998576964-0.00606987406437-0.0334345318390.2051259346220.05525503007340.17589964796820.497680649617.3938053034-18.2391923503
272.71438692865-0.2490358393940.4382954564732.36035335133-1.273379982643.239841367770.0451666574381-0.0769465569591-0.0540821558545-0.0659235549496-0.04493830185450.07168203876630.1916699178760.0099639066032-0.01669908927110.09376235244770.0202289356440.0003795483754270.061890696115-0.02770050164020.088884236964212.226490311711.601207035824.4265927255
281.388871059530.7833901947650.1875331733872.41096737965-0.4753685667291.10206951539-0.02076171544620.01949974402750.1403216470370.0148981634501-0.0608911013002-0.00120435250804-0.0423625798506-0.01182493403350.08405862776530.11917432450.0243072358738-0.006918741763210.0872351614288-0.00659925968420.13806526596113.687257836926.416101548627.7760340387
291.81379720875-1.18075211444-1.39598429644.665668956452.365597694457.13168689880.08214783311650.02613206270260.177681721052-0.0963715328175-0.02824097212170.245830758444-0.207366416884-0.165322141955-0.0830455713010.1140222912770.0322661952013-0.009125107162420.09773824436860.007886876503130.2221648110015.6441250830433.1076096523.0917187391
304.68601705373-1.960879084590.09231919109483.265233641570.5299760415440.721319400782-0.119791528791-0.1791113050650.004098064866910.3429063392010.125577587553-0.1548145568570.07076301406440.09624635567860.002926460148070.1791938261080.00613717811745-0.006568382249770.1336984046470.01300324244370.06256438932720.608893128816.004495937634.9148724331
310.977850647714-0.264932609258-0.1592938850681.479563439040.2892870054731.21542540677-0.000178410085520.07754840734130.003879283773550.005805925460740.00120275142642-0.06439641871020.04202931313460.0254963587833-0.007983048764060.08551389058650.0138713240234-0.002004576453380.08263744682470.01119758900060.11118440763922.87248077189.4369554001320.8581114121
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 104 )
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 128 )
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 186 )
7X-RAY DIFFRACTION7chain 'A' and (resid 187 through 220 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 24 )
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 42 )
10X-RAY DIFFRACTION10chain 'B' and (resid 43 through 80 )
11X-RAY DIFFRACTION11chain 'B' and (resid 81 through 104 )
12X-RAY DIFFRACTION12chain 'B' and (resid 105 through 128 )
13X-RAY DIFFRACTION13chain 'B' and (resid 129 through 154 )
14X-RAY DIFFRACTION14chain 'B' and (resid 155 through 186 )
15X-RAY DIFFRACTION15chain 'B' and (resid 187 through 197 )
16X-RAY DIFFRACTION16chain 'B' and (resid 198 through 207 )
17X-RAY DIFFRACTION17chain 'B' and (resid 208 through 220 )
18X-RAY DIFFRACTION18chain 'C' and (resid 2 through 80 )
19X-RAY DIFFRACTION19chain 'C' and (resid 81 through 104 )
20X-RAY DIFFRACTION20chain 'C' and (resid 105 through 128 )
21X-RAY DIFFRACTION21chain 'C' and (resid 129 through 144 )
22X-RAY DIFFRACTION22chain 'C' and (resid 145 through 154 )
23X-RAY DIFFRACTION23chain 'C' and (resid 155 through 186 )
24X-RAY DIFFRACTION24chain 'C' and (resid 187 through 197 )
25X-RAY DIFFRACTION25chain 'C' and (resid 198 through 207 )
26X-RAY DIFFRACTION26chain 'C' and (resid 208 through 220 )
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 24 )
28X-RAY DIFFRACTION28chain 'D' and (resid 25 through 80 )
29X-RAY DIFFRACTION29chain 'D' and (resid 81 through 104 )
30X-RAY DIFFRACTION30chain 'D' and (resid 105 through 128 )
31X-RAY DIFFRACTION31chain 'D' and (resid 129 through 220 )

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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