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- PDB-5o7a: Quinolin-6-yloxyacetamides are microtubule destabilizing agents t... -

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基本情報

登録情報
データベース: PDB / ID: 5o7a
タイトルQuinolin-6-yloxyacetamides are microtubule destabilizing agents that bind to the colchicine site of tubulin
要素
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Uncharacterized protein
キーワードMOTOR PROTEIN / Microtubules / Tubulin / Colchicine / Quinolin-6-yloxyacetamides
機能・相同性
機能・相同性情報


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / double-stranded RNA binding / 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 / neuron projection / cilium / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
類似検索 - 分子機能
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / 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 / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Chem-9N5 / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
類似検索 - 構成要素
生物種Rattus norvegicus (ドブネズミ)
Gallus gallus (ニワトリ)
Bos taurus (ウシ)
手法X線回折 / シンクロトロン / 解像度: 2.495 Å
データ登録者Sharma, A. / Olieric, N. / Steinmetz, M.O.
引用ジャーナル: Int J Mol Sci / 年: 2017
タイトル: Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin.
著者: Sharma, A. / Saez-Calvo, G. / Olieric, N. / de Asis Balaguer, F. / Barasoain, I. / Lamberth, C. / Diaz, J.F. / Steinmetz, M.O.
履歴
登録2017年6月8日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年7月5日Provider: repository / タイプ: Initial release
改定 1.12024年5月8日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)264,87717
ポリマ－261,6316
非ポリマー3,24611
水2,378132
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)104.907, 157.474, 180.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 50204.445 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P81947
#2: タンパク質 Tubulin beta-2B chain


分子量: 49999.887 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q6B856
#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) Rattus norvegicus (ドブネズミ) / 遺伝子: Stmn4 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P63043
#4: タンパク質 Uncharacterized protein


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 , 6種, 143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-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
#7: 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
#8: 化合物 ChemComp-9N5 / (2~{R})-2-(3-ethynylquinolin-6-yl)oxy-2-methoxy-~{N}-[(1~{E})-1-methoxyimino-2-methyl-propan-2-yl]ethanamide


分子量: 355.388 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C19H21N3O4
#9: 化合物 ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE / β,γ-メチレンATP


分子量: 505.208 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C11H18N5O12P3
コメント: AMP-PCP, エネルギー貯蔵分子類似体*YM
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 132 / 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: 2.85 Å3/Da / 溶媒含有率: 56.87 %
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: 6.7
詳細: 10% PEG 4000, 20% glycerol, 30 mM CaCl2, 30 mM MgCl2, 0.1 M MES/imidazole, pH 6.7, 1 mM AMPPCP, 10 mM DTT, 0.1 mM GDP

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X06DA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2014年2月24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 Å / 相対比: 1
反射解像度: 2.495→47.98 Å / Num. all: 9893 / Num. obs: 104223 / % possible obs: 100 % / 冗長度: 13.4 % / Rmerge(I) obs: 0.2069 / Net I/σ(I): 13.94
反射 シェル解像度: 2.495→2.584 Å / Rmerge(I) obs: 3.31 / CC1/2: 0.231

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解析

ソフトウェア
名称バージョン分類
PHENIX(dev_2420: ???)精密化
XDSデータ削減
XSCALEデータスケーリング
PHENIX位相決定
精密化解像度: 2.495→47.979 Å / SU ML: 0.41 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 29.34
Rfactor反射数%反射
Rfree0.2559 1999 1.92 %
Rwork0.2042 --
obs0.2051 104115 99.55 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.495→47.979 Å
タンパク質核酸リガンド溶媒全体
原子数16535 0 207 132 16874
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00917236
X-RAY DIFFRACTIONf_angle_d1.0623404
X-RAY DIFFRACTIONf_dihedral_angle_d22.2366345
X-RAY DIFFRACTIONf_chiral_restr0.0562563
X-RAY DIFFRACTIONf_plane_restr0.0063025
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4949-2.55730.37711330.36116791X-RAY DIFFRACTION94
2.5573-2.62640.35651420.32817247X-RAY DIFFRACTION100
2.6264-2.70370.36631420.31217243X-RAY DIFFRACTION100
2.7037-2.7910.33771420.29837248X-RAY DIFFRACTION100
2.791-2.89070.34021410.28797244X-RAY DIFFRACTION100
2.8907-3.00640.33281440.27017299X-RAY DIFFRACTION100
3.0064-3.14320.34051420.24837238X-RAY DIFFRACTION100
3.1432-3.30890.34681420.23657306X-RAY DIFFRACTION100
3.3089-3.51620.27531430.21627300X-RAY DIFFRACTION100
3.5162-3.78750.22791440.19147328X-RAY DIFFRACTION100
3.7875-4.16850.21741440.16457345X-RAY DIFFRACTION100
4.1685-4.77120.18711440.14377403X-RAY DIFFRACTION100
4.7712-6.00940.2181460.17867427X-RAY DIFFRACTION100
6.0094-47.98750.22991500.18347697X-RAY DIFFRACTION100
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)
12.771-0.3328-0.66643.9906-0.55711.92470.00260.12070.3542-0.26260.2457-0.3592-0.79850.3094-0.28560.7677-0.10780.15540.6098-0.15310.574628.711395.882852.6382
20.61270.26981.17162.82460.92073.8688-0.12270.25830.1003-0.55880.4801-0.5739-0.84130.4754-0.37540.6118-0.17250.21140.7101-0.23390.65335.261383.598345.7821
31.98320.7811-0.49426.62550.76121.98830.08340.1160.00860.25510.2701-0.673-0.01750.4855-0.35290.4136-0.00130.01790.5623-0.2050.490832.927477.091758.2257
44.2752-1.00632.06443.6740.07715.23930.05090.1242-0.18480.13190.09670.0631-0.19450.1736-0.13290.42210.00010.10140.438-0.11780.412720.952484.151364.9232
50.83890.93251.43672.3393-0.23488.20090.1105-0.35990.23520.3270.02350.5636-0.3908-0.5605-0.16250.5162-0.0140.16070.5229-0.12990.61639.2984.222971.7419
61.1762-0.8812-0.11654.80741.66023.3696-0.0948-0.26060.02660.88230.22840.0490.1790.28-0.09950.4469-0.02930.02230.5123-0.09650.481822.990876.73569.9368
77.7505-2.5707-1.96472.8352-2.41875.2793-0.1223-0.39031.34890.07840.34930.7279-1.02110.438-0.23680.4987-0.00260.09240.3861-0.04350.608523.307267.889625.9502
86.2578-3.2584-3.33989.06782.12493.85290.05980.60540.4157-0.593-0.17310.8908-0.5673-0.43480.12220.42960.0527-0.03840.5296-0.01290.602612.01263.153520.6187
98.7359-1.7465-3.00533.54423.22623.20760.21770.14341.4834-0.54740.07810.278-1.7429-0.3354-0.49290.86590.09130.05110.4904-0.01470.70499.716479.788721.3794
103.8039-5.01670.13717.96032.44135.51060.4471-0.48261.31080.13050.2107-0.7607-1.09810.596-0.63010.7134-0.11530.09370.5585-0.03620.736318.032277.028626.3367
112.18341.09182.12393.67444.00028.2653-0.4208-0.13011.3939-1.29620.366-0.8635-2.1003-0.66370.13680.85560.14770.12160.54430.03970.767320.352776.143617.6957
123.9275-3.964-2.06934.20042.85944.44940.45071.26690.2886-1.3683-0.53020.0204-0.8704-0.83470.06560.76740.0305-0.05230.66110.00090.596116.98562.477310.9623
133.9521-0.5186-1.59754.53522.97644.23480.1350.53550.2334-0.57090.1727-0.4929-0.67240.2592-0.32060.4455-0.03530.02250.538-0.03340.407927.59657.952518.1214
141.3631-0.38511.61894.98884.25516.5513-0.0460.1607-0.2537-0.28980.6223-0.9368-0.33510.8722-0.51250.3469-0.0310.09490.583-0.08770.638330.584454.342223.5762
154.97560.2048-1.29752.6691-0.43031.5445-0.4890.1127-0.0857-0.53870.29680.1606-0.23140.010.19210.43930.07260.04160.5257-0.09620.376319.898352.862427.2901
160.0972-0.6392-0.9863.79116.12139.9567-0.12550.29910.24390.68940.4339-0.51490.55471.1087-0.50190.3620.0983-0.01060.4551-0.03580.526723.923143.736627.3119
173.9356-2.10132.72451.4569-0.80045.45090.0534-1.1012-0.02950.3457-0.24560.63580.2566-1.08950.26110.41660.02420.04880.6383-0.21480.5578.918850.647730.1931
182.5355-2.8007-0.85083.17161.18057.6952-0.02730.01280.0933-0.2179-0.40410.8394-0.0857-1.59120.40670.36760.0835-0.04580.6229-0.12820.5933.29455.70324.814
194.4417-1.31811.99843.24440.52124.66150.0844-0.0130.3826-0.0417-0.1216-0.169-0.33680.12790.03330.3424-0.00530.090.4159-0.11030.401617.538962.754538.6254
207.7013-6.59977.25845.7785-6.45847.32160.66030.1890.4038-0.3476-0.00351.2448-0.5402-2.1077-0.27070.88520.08810.00311.036-0.11160.9603-9.89465.331134.4131
214.26164.63454.44325.05294.82274.6405-0.3680.966-0.8292-0.6064-0.29771.11370.4141-1.27350.64890.58930.05490.00710.9366-0.21510.7321-1.890660.889842.4452
224.74474.16744.25284.92213.32923.93091.34380.221-0.6657-0.63430.7796-1.2926-0.3343-0.2214-1.80170.6657-0.00240.0930.7522-0.26260.91291.440752.932140.0451
237.6257-5.89968.3624.6225-6.62659.62071.0786-0.72830.38481.0845-2.17670.52110.04151.25030.85290.4692-0.08810.13670.7405-0.22680.60227.471349.012936.7931
246.09025.74843.85037.59924.1272.57510.9815-1.22250.42451.2277-1.19380.65230.7277-1.53910.20680.7292-0.10390.10080.7222-0.13110.512310.753849.233446.7638
253.71673.1672-0.37095.3822-2.93342.5807-0.18780.55110.47520.11340.18020.3732-0.2987-0.6809-0.07270.47280.2305-0.04550.6901-0.15080.61274.410169.15440.7079
263.4656-3.9836-2.68396.55485.52515.1054-1.1115-1.2506-0.16741.2250.46960.8674-0.3064-0.07170.67450.89250.12550.10990.9815-0.2040.80272.075364.534651.3533
279.89384.30238.08563.92013.41786.80940.7158-0.95820.33980.1142-0.580.2480.52-0.6792-0.0760.62370.02650.08190.6921-0.10990.603512.970854.04153.4838
283.24420.38293.00344.6116-0.89463.20560.44990.8401-0.4944-0.95320.35470.6220.12180.3722-0.24040.57930.0834-0.00780.5761-0.11440.50137.060670.368140.0832
296.9772-4.23765.1774.0472-4.94456.0032-0.18860.35450.10970.0332-0.00330.2458-0.0832-0.48950.3350.44770.0593-0.05070.6587-0.17360.6044.795263.387635.931
302.4587-3.1285-2.93276.23627.31968.7134-0.5214-0.2774-0.24191.2289-0.17731.86131.1469-0.02290.57270.5537-0.04190.10970.4081-0.03650.53717.19536.602632.4429
319.06563.2514-3.53748.0726-0.56256.7956-0.3258-0.09020.00380.49980.4269-0.88560.33960.69710.01310.3780.0899-0.02160.4357-0.16540.494927.244834.15517.4081
325.93-3.8316-4.18437.32395.91269.3616-0.6137-0.5073-0.73631.4638-0.03730.35481.16970.90250.6870.6838-0.0901-0.06610.64030.0750.49125.21139.601237.8913
332.9964-1.5548-0.53195.40580.44252.8175-0.01110.2080.3701-0.142-0.10020.1006-0.47420.07860.09260.4767-0.0485-0.00070.47920.02950.428414.592442.4605-13.0916
343.2457-3.2927-0.39733.8098-0.76413.9970.17140.27350.1088-0.99570.0948-0.1971-0.1086-0.1938-0.21140.4171-0.13920.00740.5311-0.01220.453721.549428.4164-20.4533
351.8722-0.45650.3428.31611.7313.1547-0.03310.21320.133-0.46190.1843-0.4496-0.21620.4771-0.16550.3168-0.10740.06620.5315-0.05960.437127.734132.3624-9.5237
362.4865-3.2971-2.06418.7173-0.07863.7326-0.2811-0.031-0.06630.42590.21620.50150.08470.32820.06550.281-0.01960.03050.3249-0.0220.298520.274720.6853-3.539
379.771-0.77594.2995.02670.56053.26160.5672-0.441-1.3531-0.1142-0.24860.71820.8826-0.7727-0.31380.4732-0.08430.02590.5642-0.04280.58541.598820.9605-6.5372
381.6297-0.95740.48742.02130.29121.2001-0.07160.05060.2247-0.07630.07530.1074-0.2584-0.1747-0.00580.3732-0.020.05560.49120.00640.51248.097833.4080.6903
391.5621-1.4722-0.68542.2151.45052.49460.21060.1447-0.28140.0285-0.31780.53810.4104-0.72790.06140.5304-0.20390.0730.6534-0.13280.5566-3.142926.53345.4959
406.9177-5.73882.8065.7906-2.21434.4052-0.3042-0.341-0.02110.37650.15960.3372-0.0984-0.51630.11580.4146-0.10250.00590.511-0.15030.5659-0.77635.727512.227
415.6022-1.08385.72542.164-0.56366.7694-0.2413-0.44160.23070.04690.15980.2156-0.085-0.48460.10880.324-0.050.12720.3652-0.09050.42542.36634.30786.1533
420.6339-1.0844-0.72733.17961.41511.9673-0.21240.045-0.07570.59910.07360.23320.4358-0.02640.21390.4642-0.06090.04480.4183-0.04670.473912.545116.95723.4489
431.7964-1.8376-1.41164.51115.25686.1661-0.03890.0037-0.14240.54960.2389-0.24830.61340.352-0.31750.45140.0271-0.03810.3637-0.04110.433625.371410.9682.1042
445.3846-2.1448-1.4766.391-1.29021.4439-0.19260.7643-0.5765-0.73980.29690.60370.0207-0.5189-0.1690.6538-0.20380.01320.9312-0.07780.375317.06874.8635-40.8764
452.8192-2.08542.43979.57665.66158.98240.29920.38310.9614-1.5766-0.3862-0.0297-0.54520.0970.160.7496-0.076-0.03291.06840.18420.76998.053517.7567-45.6038
462.3086-3.2374-1.70946.81224.68897.85490.00630.56961.0433-0.17590.4804-0.3889-1.13011.2539-0.50490.6939-0.20510.03290.89420.06860.663416.503518.2056-41.8758
472.916-3.6875-0.46327.1947-1.0333.33750.12760.7127-0.2105-1.393-0.096-0.31490.5710.43870.02370.8962-0.23420.17181.2372-0.26810.589326.7426-0.9378-47.9726
484.64990.4284-1.88657.75163.3627.49220.21310.30910.1928-1.94460.3857-1.2765-0.83390.7759-0.61040.8279-0.24050.1491.0679-0.1580.626335.07426.1999-42.5273
493.31780.0395-0.91842.1701-0.64923.0967-0.18030.4591-0.3461-0.37880.244-0.14330.5011-0.1081-0.05740.6809-0.10010.07760.6756-0.22260.486220.871-5.4378-34.1768
504.8444-0.46521.87552.2003-0.02345.0116-0.12140.82380.1185-0.31590.0413-0.0293-0.01580.21280.05230.4547-0.09440.06880.5657-0.07710.390216.02524.7982-24.2057
512.2586-1.0628-2.04644.76643.70084.0659-0.46511.1955-1.0036-0.15740.20480.41510.5248-0.86570.31010.7325-0.25880.04190.9822-0.10660.6615-1.3132-3.6641-23.6915
528.01830.8625-6.23995.5352-0.87054.8570.4312-1.0124-0.15310.13570.4241-0.27390.7572-1.0125-0.99270.7209-0.3450.01040.9482-0.10390.506110.1626-10.7727-25.6129
537.31191.6955-0.87968.1388-5.81478.15820.10090.4595-0.27450.56510.5356-0.16290.9002-1.1181-0.66030.8332-0.04780.0720.5632-0.10960.486811.2199-8.4576-15.1658
548.34492.2785-0.66257.330.01314.1921-0.13311.63561.305-0.3464-0.17660.8567-0.5597-0.25370.10650.5557-0.1429-0.09870.9987-0.01330.69841.78557.7343-25.366
557.5517-4.73673.16963.0142-1.57515.0333-0.4619-0.70070.45020.57020.89630.4614-0.1588-1.3611-0.41380.69170.01020.05690.92280.0010.68780.15441.6741-13.716
568.9214-6.94044.59889.3677-0.02585.6477-0.6241-0.1251-0.31990.97510.3592-0.239-0.639-0.2780.6070.6152-0.09440.05440.5568-0.10430.5113.4888-0.5652-8.48
579.3891-3.66295.87675.8011-3.97834.3224-0.64620.79020.1115-0.23640.93590.5844-0.6119-0.5578-0.14470.5274-0.1563-0.03640.79480.10910.64114.16469.566-26.0854
582.0853-0.59370.35992.4682-0.31143.0177-0.23590.0688-0.2259-0.41220.2171-0.33890.7326-0.1174-0.00410.757-0.19090.16460.5482-0.20630.573915.4548-10.9167-26.8916
597.5162-2.3856-6.81623.92971.62857.4869-0.3522-0.0907-0.8182-0.17530.3846-0.48350.93070.69770.01780.82730.01030.04390.6028-0.23520.742330.6672-17.1162-24.4968
605.9423-4.4357-2.79929.0241.83061.1996-0.0079-0.37390.1282.02840.4194-0.8466-0.00910.509-0.59490.9733-0.1026-0.17180.6696-0.19520.730125.757194.347783.5671
610.4913-0.5357-0.8481.33090.97141.4963-0.164-0.05220.00190.06840.5678-0.33760.26430.8889-0.49340.40670.08420.03390.8216-0.2070.673242.964228.85345.1922
624.3129-0.9918-3.91088.64843.28184.3661-0.53851.0094-1.36770.08610.2316-0.30522.3526-0.4520.50331.3246-0.09910.23920.7711-0.06750.7785.149550.795369.5086
632.1934-0.1119-2.20150.0787-0.12852.8484-0.54010.734-1.5377-0.13450.9440.42321.3375-1.05440.16481.487-0.31740.41170.8352-0.31761.2473-2.294847.415973.1057
648.66493.2737-2.74157.5091-0.03117.9986-0.35870.3571-0.5906-0.01540.3962-0.35551.2971-0.2695-0.01290.77370.0350.07040.5663-0.06520.46948.420857.443868.9397
658.25263.6969-3.28728.2979-1.50157.75-0.3386-0.7934-0.3450.0888-0.2568-0.1189-0.33181.13940.52590.61750.1316-0.06290.78810.03030.505210.98564.747596.682
662.22551.56960.96253.63280.82375.41960.57160.271-0.15241.2744-0.06790.80681.38061.122-0.46261.0930.45420.14520.96330.28810.96624.384650.528109.7216
678.55372.5768-5.41057.223-3.67154.0231-0.70810.0659-0.9806-0.47660.23840.06511.5143-0.76110.45430.9171-0.04640.22840.4731-0.01930.5945-3.720856.96588.3125
685.5776-1.4254.83395.7495-2.4944.47050.08860.9844-3.1118-0.6848-0.24690.57841.29911.77570.37121.64750.35660.56621.1230.0731.592-0.008741.020697.9603
695.38452.53832.33642.33442.01261.7645-0.03250.1816-0.24460.47630.31890.63110.8463-0.7727-0.21311.2206-0.00510.29840.74460.14350.7071-13.57452.0315103.9817
705.79461.5287-4.94071.1421-0.80644.102-0.135-0.3729-0.43550.02840.0888-0.0230.52260.67420.07910.76450.11120.05210.54670.01290.52831.895762.67391.9599
716.1765-0.5517-1.01985.1877-1.5074.5424-0.46860.904-1.1821-0.30260.51910.47171.7793-0.8788-0.09641.0509-0.32260.22070.7986-0.24970.8118-5.285552.788678.2624
727.3865-5.5166-5.77257.15723.70024.62280.4132-0.4579-0.47161.043-0.63261.86670.7337-0.02680.29340.7796-0.11740.06930.81120.15570.6211-10.416860.627486.1519
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 199 )
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 273 )
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 311 )
6X-RAY DIFFRACTION6chain 'A' and (resid 312 through 437 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 9 )
8X-RAY DIFFRACTION8chain 'B' and (resid 10 through 27 )
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 42 )
10X-RAY DIFFRACTION10chain 'B' and (resid 45 through 55 )
11X-RAY DIFFRACTION11chain 'B' and (resid 56 through 66 )
12X-RAY DIFFRACTION12chain 'B' and (resid 67 through 88 )
13X-RAY DIFFRACTION13chain 'B' and (resid 89 through 144 )
14X-RAY DIFFRACTION14chain 'B' and (resid 145 through 160 )
15X-RAY DIFFRACTION15chain 'B' and (resid 161 through 180 )
16X-RAY DIFFRACTION16chain 'B' and (resid 181 through 197 )
17X-RAY DIFFRACTION17chain 'B' and (resid 198 through 215 )
18X-RAY DIFFRACTION18chain 'B' and (resid 216 through 238 )
19X-RAY DIFFRACTION19chain 'B' and (resid 239 through 275 )
20X-RAY DIFFRACTION20chain 'B' and (resid 282 through 287 )
21X-RAY DIFFRACTION21chain 'B' and (resid 288 through 295 )
22X-RAY DIFFRACTION22chain 'B' and (resid 296 through 300 )
23X-RAY DIFFRACTION23chain 'B' and (resid 301 through 306 )
24X-RAY DIFFRACTION24chain 'B' and (resid 307 through 314 )
25X-RAY DIFFRACTION25chain 'B' and (resid 315 through 324 )
26X-RAY DIFFRACTION26chain 'B' and (resid 325 through 338 )
27X-RAY DIFFRACTION27chain 'B' and (resid 339 through 350 )
28X-RAY DIFFRACTION28chain 'B' and (resid 351 through 360 )
29X-RAY DIFFRACTION29chain 'B' and (resid 369 through 381 )
30X-RAY DIFFRACTION30chain 'B' and (resid 382 through 401 )
31X-RAY DIFFRACTION31chain 'B' and (resid 402 through 414 )
32X-RAY DIFFRACTION32chain 'B' and (resid 415 through 437 )
33X-RAY DIFFRACTION33chain 'C' and (resid 1 through 72 )
34X-RAY DIFFRACTION34chain 'C' and (resid 73 through 111 )
35X-RAY DIFFRACTION35chain 'C' and (resid 112 through 161 )
36X-RAY DIFFRACTION36chain 'C' and (resid 162 through 199 )
37X-RAY DIFFRACTION37chain 'C' and (resid 200 through 223 )
38X-RAY DIFFRACTION38chain 'C' and (resid 224 through 281 )
39X-RAY DIFFRACTION39chain 'C' and (resid 282 through 311 )
40X-RAY DIFFRACTION40chain 'C' and (resid 312 through 338 )
41X-RAY DIFFRACTION41chain 'C' and (resid 339 through 372 )
42X-RAY DIFFRACTION42chain 'C' and (resid 373 through 399 )
43X-RAY DIFFRACTION43chain 'C' and (resid 400 through 440 )
44X-RAY DIFFRACTION44chain 'D' and (resid 2 through 28 )
45X-RAY DIFFRACTION45chain 'D' and (resid 29 through 42 )
46X-RAY DIFFRACTION46chain 'D' and (resid 45 through 63 )
47X-RAY DIFFRACTION47chain 'D' and (resid 64 through 109 )
48X-RAY DIFFRACTION48chain 'D' and (resid 110 through 128 )
49X-RAY DIFFRACTION49chain 'D' and (resid 129 through 238 )
50X-RAY DIFFRACTION50chain 'D' and (resid 239 through 275 )
51X-RAY DIFFRACTION51chain 'D' and (resid 286 through 300 )
52X-RAY DIFFRACTION52chain 'D' and (resid 301 through 306 )
53X-RAY DIFFRACTION53chain 'D' and (resid 307 through 314 )
54X-RAY DIFFRACTION54chain 'D' and (resid 315 through 324 )
55X-RAY DIFFRACTION55chain 'D' and (resid 325 through 342 )
56X-RAY DIFFRACTION56chain 'D' and (resid 343 through 350 )
57X-RAY DIFFRACTION57chain 'D' and (resid 351 through 360 )
58X-RAY DIFFRACTION58chain 'D' and (resid 369 through 399 )
59X-RAY DIFFRACTION59chain 'D' and (resid 400 through 441 )
60X-RAY DIFFRACTION60chain 'E' and (resid 6 through 46 )
61X-RAY DIFFRACTION61chain 'E' and (resid 47 through 141 )
62X-RAY DIFFRACTION62chain 'F' and (resid 1 through 11 )
63X-RAY DIFFRACTION63chain 'F' and (resid 12 through 24 )
64X-RAY DIFFRACTION64chain 'F' and (resid 25 through 66 )
65X-RAY DIFFRACTION65chain 'F' and (resid 67 through 96 )
66X-RAY DIFFRACTION66chain 'F' and (resid 97 through 199 )
67X-RAY DIFFRACTION67chain 'F' and (resid 200 through 222 )
68X-RAY DIFFRACTION68chain 'F' and (resid 240 through 263 )
69X-RAY DIFFRACTION69chain 'F' and (resid 264 through 283 )
70X-RAY DIFFRACTION70chain 'F' and (resid 284 through 333 )
71X-RAY DIFFRACTION71chain 'F' and (resid 334 through 362 )
72X-RAY DIFFRACTION72chain 'F' and (resid 373 through 378 )

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る