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- PDB-6kpp: BNC105 in complex with tubulin -

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基本情報

登録情報
データベース: PDB / ID: 6kpp
タイトルBNC105 in complex with tubulin
要素
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin tyrosine ligase
キーワードANTITUMOR PROTEIN / BNC105 / tubulin / protein-drug complex
機能・相同性
機能・相同性情報


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / microtubule-based process / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / microtubule cytoskeleton / growth cone / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / microtubule / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
類似検索 - 分子機能
Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. ...Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
類似検索 - ドメイン・相同性
Chem-DO6 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin tyrosine ligase / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Gallus gallus (ニワトリ)
Sus scrofa (ブタ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.74524106157 Å
データ登録者Wang, T. / Wu, C. / Pu, D.
引用ジャーナル: Biochem.Biophys.Res.Commun. / 年: 2020
タイトル: Unraveling the molecular mechanism of BNC105, a phase II clinical trial vascular disrupting agent, provides insights into drug design.
著者: Wang, T. / Wu, C. / Wang, C. / Zhang, G. / Arnst, K.E. / Yao, Y. / Zhang, Z. / Wang, Y. / Pu, D. / Li, W.
履歴
登録2019年8月15日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02020年8月19日Provider: repository / タイプ: Initial release
改定 1.12023年11月22日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
F: Tubulin tyrosine ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)264,73522
ポリマ－261,3056
非ポリマー3,43016
水2,900161
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area22170 Å2
ΔGint-111 kcal/mol
Surface area80880 Å2
単位格子
Length a, b, c (Å)105.455, 157.664, 183.135
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETLEULEU(chain 'A' and (resid 1 through 119 or resid 121...AA1 - 1191 - 119
121ARGARGTHRTHR(chain 'A' and (resid 1 through 119 or resid 121...AA121 - 150121 - 150
131LEULEUTYRTYR(chain 'A' and (resid 1 through 119 or resid 121...AA152 - 210152 - 210
141ILEILETHRTHR(chain 'A' and (resid 1 through 119 or resid 121...AA212 - 292212 - 292
151ALAALAMETMET(chain 'A' and (resid 1 through 119 or resid 121...AA294 - 313294 - 313
161LEULEUASPASP(chain 'A' and (resid 1 through 119 or resid 121...AA317 - 438317 - 438
271METMETLEULEU(chain 'C' and (resid 1 through 119 or resid 121...CC1 - 1191 - 119
281ARGARGTHRTHR(chain 'C' and (resid 1 through 119 or resid 121...CC121 - 150121 - 150
291LEULEUTYRTYR(chain 'C' and (resid 1 through 119 or resid 121...CC152 - 210152 - 210
2101ILEILETHRTHR(chain 'C' and (resid 1 through 119 or resid 121...CC212 - 292212 - 292
2111ALAALAMETMET(chain 'C' and (resid 1 through 119 or resid 121...CC294 - 313294 - 313
2121LEULEUASPASP(chain 'C' and (resid 1 through 119 or resid 121...CC317 - 438317 - 438
1132METMETGLUGLU(chain 'B' and (resid 1 through 53 or resid 57...BB1 - 531 - 53
1142ASNASNTHRTHR(chain 'B' and (resid 1 through 53 or resid 57...BB57 - 14357 - 143
1152GLYGLYLEULEU(chain 'B' and (resid 1 through 53 or resid 57...BB146 - 273146 - 273
1162LEULEUMETMET(chain 'B' and (resid 1 through 53 or resid 57...BB284 - 406284 - 406
1172PHEPHETHRTHR(chain 'B' and (resid 1 through 53 or resid 57...BB408 - 429408 - 429
2182METMETGLUGLU(chain 'D' and (resid 1 through 144 or resid 146 through 406 or resid 408 through 429))DD1 - 531 - 53
2192ASNASNTHRTHR(chain 'D' and (resid 1 through 144 or resid 146 through 406 or resid 408 through 429))DD57 - 14357 - 143
2202GLYGLYLEULEU(chain 'D' and (resid 1 through 144 or resid 146 through 406 or resid 408 through 429))DD146 - 273146 - 273
2212LEULEUMETMET(chain 'D' and (resid 1 through 144 or resid 146 through 406 or resid 408 through 429))DD284 - 406284 - 406
2222PHEPHETHRTHR(chain 'D' and (resid 1 through 144 or resid 146 through 406 or resid 408 through 429))DD408 - 429408 - 429

NCSアンサンブル:
ID
1
2

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要素

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タンパク質 , 4種, 6分子 ACBDEF

#1: タンパク質 Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


分子量: 50041.273 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: Q2XVP4
#2: タンパク質 Tubulin beta chain


分子量: 49999.887 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: A0A287AGU7, UniProt: P02554*PLUS
#3: タンパク質 Stathmin-4 / Stathmin-like protein B3 / RB3


分子量: 16844.162 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Stmn4 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P63042
#4: タンパク質 Tubulin tyrosine ligase


分子量: 44378.496 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Gallus gallus (ニワトリ) / 遺伝子: TTL / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: E1BQ43

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非ポリマー , 8種, 177分子

#5: 化合物 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM
#6: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mg
#7: 化合物 ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Ca
#8: 化合物 ChemComp-DO6 / (6-methoxy-2-methyl-7-oxidanyl-1-benzofuran-3-yl)-(3,4,5-trimethoxyphenyl)methanone / 2-メチル-3-(3,4,5-トリメトキシベンゾイル)-6-メトキシ-7-ヒドロキシベンゾフラン


分子量: 372.369 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C20H20O7 / タイプ: SUBJECT OF INVESTIGATION
#9: 化合物 ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / コメント: GDP, エネルギー貯蔵分子*YM
#10: 化合物 ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / 2-モルホリノエタンスルホン酸


分子量: 195.237 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H13NO4S / コメント: pH緩衝剤*YM
#11: 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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#12: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 161 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 3.08 Å3/Da / 溶媒含有率: 60.09 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.7
詳細: 6% PEG, 5% glycerol, 0.1M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7

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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: SSRF / ビームライン: BL19U1 / 波長: 0.9785 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年6月15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: 0.9785 Å / 相対比: 1
反射解像度: 2.74→50 Å / Num. obs: 79756 / % possible obs: 98.72 % / 冗長度: 6.6 % / Biso Wilson estimate: 45.3494782657 Å2 / CC1/2: 0.989 / Net I/σ(I): 20.3
反射 シェル解像度: 2.75→2.8 Å / Num. unique obs: 7408 / CC1/2: 0.715 / % possible all: 93.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
HKL-3000データ削減
SCALAデータスケーリング
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4I55

4i55


解像度: 2.74524106157→48.2656461817 Å / SU ML: 0.30000744212 / 交差検証法: FREE R-VALUE / σ(F): 1.35039005021 / 位相誤差: 23.6704504182
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.234792706359 4015 5.060116452 %
Rwork0.194280154566 75331 -
obs0.196346564371 79346 98.7443220708 %
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: 59.6130080251 Å2
精密化ステップサイクル: LAST / 解像度: 2.74524106157→48.2656461817 Å
タンパク質核酸リガンド溶媒全体
原子数17168 0 216 161 17545
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0034006438355417805
X-RAY DIFFRACTIONf_angle_d0.73810838906724138
X-RAY DIFFRACTIONf_chiral_restr0.04644354585122618
X-RAY DIFFRACTIONf_plane_restr0.004842626059523177
X-RAY DIFFRACTIONf_dihedral_angle_d18.48668552810699
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.77750.321255527871190.2712591231242266X-RAY DIFFRACTION86.9803063457
2.7775-2.81140.2851350152831260.2739278890682468X-RAY DIFFRACTION95.8610495196
2.8114-2.8470.3164719656251280.2597782775972567X-RAY DIFFRACTION98.2142857143
2.847-2.88440.3240739935761250.2705235483072566X-RAY DIFFRACTION99.2622648469
2.8844-2.9240.2828106959641580.2591110152642599X-RAY DIFFRACTION99.7106690778
2.924-2.96570.3454367362811460.2554683414782596X-RAY DIFFRACTION99.7453619498
2.9657-3.010.2842236239551420.2379444392472592X-RAY DIFFRACTION99.9269005848
3.01-3.0570.2752395242741370.2410831536962590X-RAY DIFFRACTION99.9267130817
3.057-3.10710.263540396341290.2335355898892650X-RAY DIFFRACTION99.9280834232
3.1071-3.16070.3014394426441240.2237205544952570X-RAY DIFFRACTION99.9258160237
3.1607-3.21810.3110716258121150.2381069111112670X-RAY DIFFRACTION99.9641062455
3.2181-3.280.2756918848951340.2370005270852575X-RAY DIFFRACTION99.8157700811
3.28-3.3470.2783524007531600.2286728352692578X-RAY DIFFRACTION99.9270072993
3.347-3.41970.2807868087711270.2192446919752641X-RAY DIFFRACTION99.8917358354
3.4197-3.49930.2559613169881600.2005161242652587X-RAY DIFFRACTION99.8545983279
3.4993-3.58670.2338973112781310.1933504173042624X-RAY DIFFRACTION99.7826874321
3.5867-3.68370.2025090999261480.1905585554072596X-RAY DIFFRACTION99.8544395924
3.6837-3.7920.2262935487321280.1843602635912620X-RAY DIFFRACTION99.6374184191
3.792-3.91440.2251731773831610.1741015706082612X-RAY DIFFRACTION99.6764917326
3.9144-4.05420.2158701293421380.1628908203022642X-RAY DIFFRACTION99.6773036931
4.0542-4.21640.1807610503911380.1637191317322598X-RAY DIFFRACTION99.6358339403
4.2164-4.40820.1907531215991610.1575199567722602X-RAY DIFFRACTION99.5317002882
4.4082-4.64050.1909889996661400.146652516232626X-RAY DIFFRACTION99.2821249103
4.6405-4.93090.1736198524661490.1498566745172613X-RAY DIFFRACTION99.0319110792
4.9309-5.31120.1941985879071250.1661216612572632X-RAY DIFFRACTION98.9946140036
5.3112-5.84490.2502298138731360.1906615413912667X-RAY DIFFRACTION98.6971830986
5.8449-6.68870.2455971315131360.1988142112312612X-RAY DIFFRACTION97.793594306
6.6887-8.41980.2327120065471570.1776773868672642X-RAY DIFFRACTION97.6963350785
8.4198-48.2650.2077282336751370.1846323549292730X-RAY DIFFRACTION95.6304202802
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)
11.68427138817-0.1236598725930.1103622454153.371717362871.025748324651.99633583722-0.1361735820760.2158336127520.286340348714-0.3826093269940.358718913224-0.352934391153-0.8291548494860.415890719066-0.3184924062230.629634430954-0.1730761542440.1336832103490.469561298456-0.1392700829570.34732370565229.413123020297.837788201354.5322089142
21.57591194237-0.248696015897-0.4808962622523.743218557871.103298180142.550668343530.05098445620250.5847191359560.103488100893-1.11676315680.315530966877-0.507153821471-0.8704183785950.298603077577-0.3212873593540.654722182438-0.1510724980380.1237415260230.53917713356-0.1630169803030.32694157894128.475100945587.618486482142.7396406328
30.585936763684-0.0313349245536-0.1954904532872.856525788731.151656124491.60879291474-0.01248746789260.255848387587-0.159531698531-0.09150716737690.541328344637-0.738717096361-0.178859981210.721069738608-0.293646504120.34073739472-0.06023242540640.04626738265970.541217854622-0.327026457830.4676487821135.017711707678.488298136155.0421822302
46.08770386388-1.281402420251.749744164784.890929282380.5942129036794.700171259790.2792104632980.013669723373-0.524731807714-0.0329991948240.05078186930450.4614675200050.122890730418-0.507310780515-0.1732524715740.265671462678-0.007906328517160.03617440974630.289123818274-0.1428434050550.25945192470113.33522756979.872033694360.5614228364
51.3615283358-0.1340230377310.4229283039573.033396649990.7949610871733.01409961059-0.1791007361150.1500198824850.03906208129140.1057456506360.219541908952-0.293976109172-0.572411976960.247271857436-0.04864166683350.379104588372-0.04054048710190.08845683982630.309475397314-0.1294946562210.2695988628925.218347758190.755062752365.7436159002
61.595387390110.844464708674-0.6959805198793.03386293631.76059661764.620924690870.270563166952-0.2011562793110.06259295588170.2709903206430.001764057303050.0976407958133-0.33375269137-0.215000105606-0.1948032234450.424254773006-0.05124010770090.1054422317330.331842638124-0.1249716638160.17870057735715.026995749686.132709930769.4043672787
71.32916338695-0.871098097345-0.02438389139924.127370399051.638479961611.316732468130.039244378054-0.2301783970070.004501488949430.785277513913-0.02098034333170.304069443034-0.01226808569860.0914477157099-0.04096824032820.5507194972120.02068634309340.1365524353610.316441474085-0.08201889963310.33592510258815.244462530585.646567844378.362268605
81.02954731618-0.478052504936-0.4017650206313.245673102861.580635658032.78135278801-0.0873672761522-0.0869367959526-0.1241930938740.7672524491460.273128977549-0.1256640590880.3527365343150.481566707021-0.2048633222350.3113943315340.0375710814638-0.05056170678630.331578175533-0.1424915685780.3014652991324.487235212773.643440472267.2878591762
94.91124723316-2.252857404880.005000466846247.52529801360.4074062580743.320184533160.2678988914660.2508634246290.915837301043-0.664400358352-0.1808192581780.000980579858962-0.9046862824-0.152354014567-0.04602975004470.433492097660.02666237071940.09564246053160.2865563443250.003394637136350.41416613297916.180041295470.452939617418.648760466
102.04984490092-0.951219637182-0.5066814520672.204162786970.8596816778892.703329276160.0434371706780.1069588861430.195925875437-0.0593168045274-0.08110276495880.111639464367-0.2638309435110.004662049870160.01488034835470.193069484407-0.01551212428380.01898814835420.270189806642-0.1242439004770.27008139913720.121388420154.522506062423.0837536444
112.548529492-0.853593137794-0.715016564324.268972639880.3802797894182.47234690681-0.03565299176950.00992086051494-0.01558479917260.06660591331180.05764007010460.526831019894-0.236299670256-0.6464937790680.0570895478920.3218691886060.06410384121390.04903840529040.491842743101-0.2390057311840.3532143132667.3949415130662.299779491340.1084214101
120.943124240759-1.03959819694-0.4261374019793.835562096632.452652387513.23017283696-0.0571265750936-0.2186582128250.1029768848930.5711219703870.01679899980080.07603692114360.3095073140430.0482677830408-0.005728897208080.185864941368-0.02968392927320.01681125687830.316598059023-0.04696897257550.26398921853317.152451920847.120065307135.7810489935
133.5237654396-2.83181849897-0.566475409176.140596889960.714277522541.860275426840.005925476182230.4218620080210.24658201573-0.610512957108-0.1062769527270.130089165832-0.340830242566-0.01672024518330.07350526979240.325787225237-0.100966769381-0.01586044500750.3106556721130.06161420761490.16951246939415.471393120239.1153664679-16.1478382279
141.4950917061-0.463136850897-0.4641250430294.91255214626-0.01446525806123.28166986837-0.16525955520.1631684641590.104511067128-0.285775474860.177496368139-0.2479581733740.0506865753250.254630386806-0.02304186565090.120626970585-0.04113476601220.01614024092410.248321471027-0.05437618827420.16516472584424.667466962726.3726392508-7.82281584898
152.47781194711-0.9165585398450.7300636550811.425407726620.04882789821492.299095324850.0859090028120.0928732730651-0.140838619524-0.0156773289027-0.1451271377490.3007430723430.0616180585331-0.4786009367480.02806176447430.186775652153-0.04397577066150.04198369668530.271663657816-0.07561829101680.2590286186613.4008532878729.09625642420.422081242308
161.98323766417-0.959265812875-0.2003210351082.674289592990.7821643722041.62000971915-0.176030223166-0.0607244572946-0.03508470511620.1663361874770.02556428784170.1599064232140.181664823006-0.08557103893360.1326257372070.182323173913-0.08591890073950.01160247860370.161759455167-0.05501434473920.18587343754510.804601530623.67391662035.92614332428
173.17682522892-0.987965666081-1.47656630513.095797989342.553591634163.18200049734-0.1000566081810.686079005158-0.182608791139-0.6965920347530.01366603129990.217303732902-0.0147417229985-0.6596852609310.1130374567531.02423447902-0.421217447590.002492710767051.08220112739-0.1165210915140.2649771868818.05763139463.68215944434-39.9557937199
184.95476110042-2.17439659828-2.521288316495.217462946274.391117351653.815432567250.09830144533151.264878537480.774896744216-1.66956890101-0.1860314048120.391487940418-0.602332691274-0.9623787165890.04751363690021.19765470405-0.223672674649-0.1172227712681.326251694140.1683449159340.55974228268213.592870396116.243969309-42.193595093
190.419784263062-0.241551102732-0.1197173565090.341164059462-0.08513709208260.1555670091930.08327677878220.723795168002-0.279988756734-0.675246558063-0.155729659567-0.02647221415830.177041188145-0.2043235223420.007988696509411.48125585926-0.4227231237540.3959974292981.27309493195-0.585940537350.42209829389529.7368781362-1.10648315019-45.5984723409
201.932353991010.3472049364370.2021759240291.70811688071.456754949572.80414290359-0.3479164935280.478284237012-0.292948267169-0.4697193482210.299128985931-0.3025169652530.2166475992970.0388374778222-0.1428615069660.909231245543-0.2879349378070.2207429408310.767891086882-0.2997384330730.39915261822627.1680465052-1.69754595199-33.4030977948
211.09195748558-0.01098802144660.866183251551.657239973651.303468615832.63135496021-0.1413495590950.457449191218-0.54553297197-0.217615086106-0.03572636700950.1314050535370.751666830723-0.310394774905-0.04376201899490.945143799454-0.2884873401870.3047097961780.687246619679-0.4729963742190.57460111483220.5677015524-12.0680141677-30.2651473029
221.717048815941.045870953862.21540349922.620310743463.096573256755.08842952002-0.3727273413460.622884993336-0.34572427383-0.8893436964030.1327753236680.3430051631330.00592740754356-0.5377187958140.3424362995210.725511081952-0.2752024168020.07886407960010.757884053911-0.2316048083370.40208777392713.47100356580.313225996062-29.3103334195
230.632876077129-1.48239501354-0.2817326267344.22925725919-0.3333585040191.44121571506-0.1285730355190.277052652181-0.3861752257-0.5342257756380.09337171512551.066833061070.690131532369-0.7305609779910.07405590747930.706761607265-0.314638577644-0.02396772156850.747906219451-0.2895053938220.6925334668474.72232892371-6.49374850148-23.0569577329
247.61725985243-2.51199786181-1.469462712548.959890952890.955009302938.52037239681-0.6413961775530.8032260800880.005597142203220.00193706089250.6266614189621.33972067607-0.353686012193-1.34982374853-0.003893375148060.41802889113-0.121047209589-0.06335898121870.6087865785560.03868951754090.4910108604541.202979011614.03508989253-18.2180644845
252.67126500324-0.668549550624-0.4632938670164.285579789161.104293440882.10344779069-0.1261407311440.673811869791-0.0338339828728-0.4117375227390.05247227883050.5056892715580.490310125116-0.6455262277920.1753189510170.362067384042-0.1285163992520.03153240219860.560524704129-0.1011839435110.3863187117016.434689136972.60875720368-19.1050852571
261.94857118853-1.08919597972-0.8765907786422.489358699810.9695986759651.26004413394-0.1459456979630.485634124741-0.792461517035-0.3567120085990.053326772301-0.2479948747030.8584287708340.235553279015-0.0279367305941.03168656317-0.02360470453750.3463206102120.52808758798-0.4822756444170.76338094133325.6587031977-16.334036499-23.3514676605
274.15294254744-2.70180852556-0.05297303814646.808326064030.9502947676261.021448350490.238590932253-0.2700913314210.2011293105161.23485750920.319213341503-0.4791395848680.3113062802550.603567710091-0.5250681253430.73697251592-0.0951211825834-0.1368442710530.570882669428-0.2016647986240.40036340516227.640401733192.854268657982.5438990002
280.6377792068940.0875305096553-0.2227640610060.137485257465-0.151337125250.234121488864-0.191848923676-0.0197105510088-0.0404512957530.1779147582940.680737851712-0.5861414727960.3782502508780.849675886072-0.598004540950.44140883070.1022717691780.07539469123980.627845226818-0.2294407110870.62620898874242.725194562727.45698137174.61380347017
293.447063474550.315368737589-0.5529253909052.38458609199-0.2788085631652.47580836905-0.304465162516-0.114227215142-0.758413459016-0.05148814666230.0553400418325-0.2143985692361.21645700913-0.05809157827280.03383765906090.786032621780.005203974748650.1687282970840.337387061847-0.01646616775890.5419077472468.0978369811358.05851665979.4750400043
300.110376029582-0.0865436627874-0.690566286651.355229226540.3586901612654.43199975597-0.187167250083-0.485784267024-0.5136070681440.6107513692020.123600377556-0.8034319153590.6668672159261.553834248540.155093463841.037909835770.396757390794-0.05116490690721.181717115850.3564432787870.850299838215.235361815555.247238373111.329260645
311.578714225431.046359426530.5402164234582.3804754001-1.606250658222.5191293621-0.30935793285-0.303867494913-0.9124226861940.3837757701420.219867029797-0.2068728882610.8548007521820.177030231532-0.2465741748171.204823317760.2566306173010.3064604343930.44161314210.2167530776150.814333068052-0.16482555099650.253300829397.8863069605
320.5592320132391.24394354588-0.3900695038462.86128356154-0.683322407590.624770797838-0.649054380057-0.339344335938-1.43692853625-0.348969313090.0981297278542-0.4790346516130.95882137720.5559111908580.5364297915791.590787697530.1584508428270.5631168919920.6724651985520.230997037111.40240244394-2.9097566494241.6618102147101.007260316
333.357225949391.68188867937-2.514480114131.32305477553-0.4347599746223.46356525234-0.420309605725-0.0732702801454-0.5239987344980.1818338257480.3089761334720.05839450956910.5626002014070.03371161741440.08551460191280.8032613326860.1010645294480.1721478359750.3586123876110.1126396888830.507651898313-0.91455493480959.413303262290.6543779843
347.59132368406-3.18192611255-2.326237828664.2818243635-1.199946760814.97838769672-0.1749752513290.74830596231-0.2123550170060.06488137460030.04923549049970.81932387340.770419195957-1.498900407450.1924688007940.411555581063-0.2204629079580.05895327291130.6133216846280.06209003997090.608188205058-9.5927604924661.992781295477.3959011876
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 197 )
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 223 )
5X-RAY DIFFRACTION5chain 'A' and (resid 224 through 259 )
6X-RAY DIFFRACTION6chain 'A' and (resid 260 through 287 )
7X-RAY DIFFRACTION7chain 'A' and (resid 288 through 338 )
8X-RAY DIFFRACTION8chain 'A' and (resid 339 through 438 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 86 )
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 236 )
11X-RAY DIFFRACTION11chain 'B' and (resid 237 through 336 )
12X-RAY DIFFRACTION12chain 'B' and (resid 337 through 429 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 102 )
14X-RAY DIFFRACTION14chain 'C' and (resid 103 through 197 )
15X-RAY DIFFRACTION15chain 'C' and (resid 198 through 311 )
16X-RAY DIFFRACTION16chain 'C' and (resid 312 through 441 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 27 )
18X-RAY DIFFRACTION18chain 'D' and (resid 28 through 62 )
19X-RAY DIFFRACTION19chain 'D' and (resid 63 through 125 )
20X-RAY DIFFRACTION20chain 'D' and (resid 126 through 178 )
21X-RAY DIFFRACTION21chain 'D' and (resid 179 through 213 )
22X-RAY DIFFRACTION22chain 'D' and (resid 214 through 264 )
23X-RAY DIFFRACTION23chain 'D' and (resid 265 through 309 )
24X-RAY DIFFRACTION24chain 'D' and (resid 310 through 336 )
25X-RAY DIFFRACTION25chain 'D' and (resid 337 through 362 )
26X-RAY DIFFRACTION26chain 'D' and (resid 363 through 431 )
27X-RAY DIFFRACTION27chain 'E' and (resid 4 through 44 )
28X-RAY DIFFRACTION28chain 'E' and (resid 45 through 141 )
29X-RAY DIFFRACTION29chain 'F' and (resid 1 through 115 )
30X-RAY DIFFRACTION30chain 'F' and (resid 116 through 192 )
31X-RAY DIFFRACTION31chain 'F' and (resid 193 through 236 )
32X-RAY DIFFRACTION32chain 'F' and (resid 237 through 275 )
33X-RAY DIFFRACTION33chain 'F' and (resid 276 through 354 )
34X-RAY DIFFRACTION34chain 'F' and (resid 355 through 380 )

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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