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- PDB-5q04: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 5q04
タイトルHuman liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(4-bromo-5-chlorothiophen-2-yl)sulfonyl-3-(5-bromo-1,3-thiazol-2-yl)urea
要素Fructose-1,6-bisphosphatase 1フルクトース-1,6-ビスホスファターゼ
キーワードHYDROLASE/HYDROLASE INHIBITOR / D3R docking / HYDROLASE-HYDROLASE INHIBITOR complex
機能・相同性
機能・相同性情報


cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process / fructose metabolic process / 糖新生 / monosaccharide binding / negative regulation of glycolytic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / AMP binding / 脱リン酸化 / cellular response to cAMP / response to nutrient levels / 糖新生 / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / metal ion binding / 細胞核 / 細胞質基質 / 細胞質
類似検索 - 分子機能
フルクトース-1,6-ビスホスファターゼ / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...フルクトース-1,6-ビスホスファターゼ / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-95P / Fructose-1,6-bisphosphatase 1 / Fructose-1,6-bisphosphatase 1
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: 2.502 Å
Model detailsFor D3R project
データ登録者Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G. / Yang, H. / Shao, C. / Burley, S.K.
引用ジャーナル: To be published
タイトル: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(4-bromo-5-chlorothiophen-2-yl)sulfonyl-3-(5- ...タイトル: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(4-bromo-5-chlorothiophen-2-yl)sulfonyl-3-(5-bromo-1,3-thiazol-2-yl)urea
著者: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.
履歴
登録2017年4月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年1月9日Provider: repository / タイプ: Initial release
改定 1.12019年1月16日Group: Data collection / カテゴリ: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
改定 1.22019年2月6日Group: Data collection / Database references / Structure summary
カテゴリ: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
改定 1.32021年2月10日Group: Structure summary / カテゴリ: audit_author / Item: _audit_author.identifier_ORCID
改定 1.42024年3月6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 / 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: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)298,72816
ポリマ-294,8758
非ポリマー3,8538
6,612367
1
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,3648
ポリマ-147,4384
非ポリマー1,9264
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area15900 Å2
ΔGint-78 kcal/mol
Surface area43770 Å2
手法PISA
2
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,3648
ポリマ-147,4384
非ポリマー1,9264
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area15830 Å2
ΔGint-79 kcal/mol
Surface area43570 Å2
手法PISA
単位格子
Length a, b, c (Å)66.281, 286.676, 83.272
Angle α, β, γ (deg.)90.000, 97.680, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 9 through 61 or resid 72 through 139 or resid 141 through 335))
21(chain B and (resid 9 through 139 or resid 141 through 335))
31(chain C and (resid 9 through 139 or resid 141 through 335))
41(chain D and (resid 9 through 139 or resid 141 through 335))
51(chain E and (resid 9 through 61 or resid 72 through 139 or resid 141 through 335))
61(chain F and (resid 9 through 139 or resid 141 through 335))
71(chain G and (resid 9 through 139 or resid 141 through 335))
81(chain H and (resid 9 through 139 or resid 141 through 335))

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
11ASPASPGLYGLY(chain A and (resid 9 through 61 or resid 72 through 139 or resid 141 through 335))AA9 - 6110 - 62
12LYSLYSTYRTYR(chain A and (resid 9 through 61 or resid 72 through 139 or resid 141 through 335))AA72 - 13973 - 140
13LYSLYSSERSER(chain A and (resid 9 through 61 or resid 72 through 139 or resid 141 through 335))AA141 - 335142 - 336
21ASPASPTYRTYR(chain B and (resid 9 through 139 or resid 141 through 335))BB9 - 13910 - 140
22LYSLYSSERSER(chain B and (resid 9 through 139 or resid 141 through 335))BB141 - 335142 - 336
31ASPASPTYRTYR(chain C and (resid 9 through 139 or resid 141 through 335))CC9 - 13910 - 140
32LYSLYSSERSER(chain C and (resid 9 through 139 or resid 141 through 335))CC141 - 335142 - 336
41ASPASPTYRTYR(chain D and (resid 9 through 139 or resid 141 through 335))DD9 - 13910 - 140
42LYSLYSSERSER(chain D and (resid 9 through 139 or resid 141 through 335))DD141 - 335142 - 336
51ASPASPGLYGLY(chain E and (resid 9 through 61 or resid 72 through 139 or resid 141 through 335))EE9 - 6110 - 62
52LYSLYSTYRTYR(chain E and (resid 9 through 61 or resid 72 through 139 or resid 141 through 335))EE72 - 13973 - 140
53LYSLYSSERSER(chain E and (resid 9 through 61 or resid 72 through 139 or resid 141 through 335))EE141 - 335142 - 336
61ASPASPTYRTYR(chain F and (resid 9 through 139 or resid 141 through 335))FF9 - 13910 - 140
62LYSLYSSERSER(chain F and (resid 9 through 139 or resid 141 through 335))FF141 - 335142 - 336
71ASPASPTYRTYR(chain G and (resid 9 through 139 or resid 141 through 335))GG9 - 13910 - 140
72LYSLYSSERSER(chain G and (resid 9 through 139 or resid 141 through 335))GG141 - 335142 - 336
81ASPASPTYRTYR(chain H and (resid 9 through 139 or resid 141 through 335))HH9 - 13910 - 140
82LYSLYSSERSER(chain H and (resid 9 through 139 or resid 141 through 335))HH141 - 335142 - 336

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要素

#1: タンパク質
Fructose-1,6-bisphosphatase 1 / フルクトース-1,6-ビスホスファターゼ / Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6- ...Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6-bisphosphatase 1 (FBP1) / mRNA


分子量: 36859.418 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FBP1, hCG_1640493 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q2TU34, UniProt: P09467*PLUS, fructose-bisphosphatase
#2: 化合物
ChemComp-95P / 4-bromo-N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-5-chlorothiophene-2-sulfonamide


分子量: 481.592 Da / 分子数: 8 / 由来タイプ: 合成 / : C8H4Br2ClN3O3S3
#3: 水 ChemComp-HOH / water /


分子量: 18.015 Da / 分子数: 367 / 由来タイプ: 天然 / : 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: 2.75 Å3/Da / 溶媒含有率: 55.22 %
結晶化温度: 300 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 0.1M HEPES pH 7.0, 0.1M AMMONIUM ACETATE, 12%-25% PEG 3350

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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: X10SA / 波長: 0.987 Å
検出器タイプ: MAR CCD 165 mm / 検出器: CCD / 日付: 2005年10月17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: 0.987 Å / 相対比: 1
反射解像度: 2.502→29.235 Å / Num. obs: 100143 / % possible obs: 94.92 %

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
PHENIX1.11.1_2575精密化
PDB_EXTRACT3.23データ抽出
精密化構造決定の手法: 分子置換 / 解像度: 2.502→29.235 Å / SU ML: 0.36 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 27.36 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2511 5006 5 %
Rwork0.1857 95137 -
obs0.189 100143 94.92 %
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 max: 153.54 Å2 / Biso mean: 51.162 Å2 / Biso min: 13.39 Å2
精密化ステップサイクル: final / 解像度: 2.502→29.235 Å
タンパク質核酸リガンド溶媒全体
原子数19440 0 160 367 19967
Biso mean--71.86 44.84 -
残基数----2540
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00819985
X-RAY DIFFRACTIONf_angle_d1.06927009
X-RAY DIFFRACTIONf_chiral_restr0.0623054
X-RAY DIFFRACTIONf_plane_restr0.0073450
X-RAY DIFFRACTIONf_dihedral_angle_d11.03212137
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsタイプ
11A12203X-RAY DIFFRACTION10.536TORSIONAL
12B12203X-RAY DIFFRACTION10.536TORSIONAL
13C12203X-RAY DIFFRACTION10.536TORSIONAL
14D12203X-RAY DIFFRACTION10.536TORSIONAL
15E12203X-RAY DIFFRACTION10.536TORSIONAL
16F12203X-RAY DIFFRACTION10.536TORSIONAL
17G12203X-RAY DIFFRACTION10.536TORSIONAL
18H12203X-RAY DIFFRACTION10.536TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5017-2.53010.382940.34911585167948
2.5301-2.55990.41041360.28112830296685
2.5599-2.59110.32991610.27782899306086
2.5911-2.62390.31481720.25512847301986
2.6239-2.65840.29871380.25592964310289
2.6584-2.69480.33541520.25223014316690
2.6948-2.73320.30471830.24392991317492
2.7332-2.7740.37091500.24633168331892
2.774-2.81730.30521550.22933099325495
2.8173-2.86350.3321720.22893222339496
2.8635-2.91280.30591650.21493238340397
2.9128-2.96570.27841860.20993245343198
2.9657-3.02270.2841840.20413304348899
3.0227-3.08430.29671780.20093315349399
3.0843-3.15130.29641870.204833213508100
3.1513-3.22450.26211980.194332863484100
3.2245-3.30510.28651760.190733623538100
3.3051-3.39430.26711880.184532583446100
3.3943-3.4940.26451810.177733893570100
3.494-3.60660.23821720.173232993471100
3.6066-3.73530.271620.172933363498100
3.7353-3.88450.19651690.17333823551100
3.8845-4.06090.23221780.159833083486100
4.0609-4.27430.19661700.159633413511100
4.2743-4.54120.21231750.155233493524100
4.5412-4.89030.18951600.144633823542100
4.8903-5.37970.23991580.167533393497100
5.3797-6.15190.24621750.189533423517100
6.1519-7.72690.24631590.191833813540100
7.7269-29.23720.19641720.1613341351398
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0285-0.1018-0.08890.1892-0.10250.1735-0.1322-0.00780.002-0.081-0.04480.0087-0.09230.148700.2709-0.04590.00580.27080.01540.262637.295614.7634-4.8712
20.1457-0.13720.02810.21460.00180.3737-0.096-0.05940.0744-0.25090.05660.1025-0.15610.11510.03950.32710.0195-0.08180.18280.02890.253122.434522.8828-8.0105
30.8597-0.2729-0.02350.13190.01970.00760.0372-0.16760.2759-0.11050.04080.0411-0.0684-0.01220.18260.57480.0189-0.16410.14680.05360.277518.399731.3863-10.3664
40.0105-0.00770.00440.01190.00520.0039-0.0344-0.0255-0.06410.21180.1471-0.05360.10650.0676-00.3210.00550.04680.398-0.00380.342722.08760.907831.3315
50.0289-0.09670.02740.58450.00090.0244-0.1402-0.0584-0.1573-0.1838-0.1030.13150.1058-0.012-0.18950.11450.01370.04530.2446-0.00030.352115.7747-3.28248.7471
60.010.0270.02050.07560.06890.0725-0.34750.1154-0.317-0.2402-0.16470.18380.1839-0.1254-0.01480.25690.01350.040.38190.02640.5031.3649-5.463215.5689
70.04440.08970.0960.43970.22850.6742-0.01610.1033-0.2753-0.2275-0.20230.1516-0.1897-0.0735-0.1570.19540.05790.08920.34840.05010.47657.73691.304712.0618
80.0302-0.1143-0.02990.19910.07170.0387-0.13180.0320.05220.08070.10350.0267-0.0936-0.071-0.00190.16920.05020.01340.30180.00410.297411.52318.705820.8957
9-0.0059-0.0086-0.00260.0092-0.0110.12-0.0485-0.0634-0.0669-0.07190.13760.2856-0.41140.0997-0.00030.45740.108-0.10150.2477-0.07560.4633.47832.19659.6755
100.0054-0.0244-0.00940.06970.03980.0342-0.0106-0.06020.0049-0.08760.12860.393-0.1469-0.07440.00210.20610.0409-0.07580.28110.0090.43254.354516.988714.894
110.04140.03230.08110.06080.12190.7376-0.20740.0617-0.14420.16450.13070.2593-0.3256-0.0696-0.0931-0.04880.47990.1130.2628-0.11930.3965-1.982121.351220.4002
120.1156-0.171-0.05150.25160.20490.1596-0.03710.03990.0068-0.3340.06370.1408-0.0941-0.13560.02970.2153-0.00460.02980.18960.00880.19336.3574-9.1349-11.2612
130.3892-0.27460.06010.3505-0.10.2034-0.01210.0306-0.0272-0.14360.0065-0.01210.09440.0814-0.00010.1946-0.00460.0410.24690.01020.2154.0806-18.932-6.8492
140.0139-0.0544-0.02240.20280.06610.02480.0702-0.09960.0819-0.1305-0.06670.3399-0.176-0.1685-0.00860.2597-0.06360.05710.41420.12070.311619.7884-13.464326.608
150.16120.06730.01650.06390.04760.0521-0.1543-0.0465-0.13710.28710.2262-0.17930.0561-0.030.01190.27850.020.04070.24480.02680.197332.7573-5.557722.9792
160.1930.15410.16070.14490.07660.3075-0.0109-0.0978-0.0522-0.0453-0.1848-0.0631-0.114-0.0264-0.17460.24190.01160.06170.16740.04770.235242.46151.926416.6009
170.0268-0.01920.02450.0064-0.01160.0210.17580.1120.17030.10890.06660.0514-0.27760.1556-0.00020.33120.0483-0.00090.2972-0.05490.326944.0086-4.407534.0176
180.08720.04170.04180.1766-0.04490.0584-0.0092-0.008-0.03010.011-0.0303-0.0311-0.0216-0.140200.1978-0.00420.05440.18510.01680.169439.736-12.426528.6508
190.0043-0.01710.03710.0486-0.02080.11380.04530.02170.1161-0.0013-0.0136-0.09750.154-0.00530.00030.20270.0130.01890.26240.01730.33733.0393-21.606514.9371
200.7927-0.3915-1.02890.1940.49871.3464-0.42330.0423-0.032-0.0656-0.15740.05980.1791-0.0864-0.30310.25120.0833-0.06740.35410.07640.297357.7975-34.338115.905
210.7081-0.04230.18070.0055-0.01190.0512-0.13170.05230.1606-0.0124-0.117-0.00180.3326-0.0733-0.05020.40390.03470.0370.25580.00280.21348.9595-35.3888.8773
22-0.01040.00050.0180.0617-0.05350.00660.0036-0.01430.20430.34310.01880.00930.1580.030.00150.19990.0085-0.01380.2497-0.00510.309746.7625-23.544222.1962
230.02820.0291-0.05150.0125-0.03030.0465-0.0671-0.0939-0.02040.03630.0437-0.00550.08270.27330.00010.2120.0541-0.01110.28180.02830.185348.5883-30.818727.749
240.28790.19750.18110.3423-0.05830.1783-0.0409-0.0918-0.15790.0749-0.0807-0.0738-0.15430.2278-0.00010.24580.0343-0.05860.27550.03350.2874-1.842254.789441.7628
250.09510.0337-0.02750.0787-0.03890.0381-0.0685-0.0285-0.24990.07160.1019-0.1430.12090.1253-00.55080.0649-0.06620.3910.04030.44552.228841.263445.8307
260.50930.0425-0.29180.0736-0.0170.1765-0.12490.0343-0.24320.19750.07480.03090.1494-0.0068-0.23770.43370.0119-0.0010.22740.10920.3911-4.696540.067345.3328
270.221-0.1327-0.10680.13550.07090.12460.00580.0085-0.1240.0589-0.02120.0812-0.1171-0.1320.00020.264-0.0230.00810.28960.01780.3353-23.269645.556839.4728
280.05180.0294-0.01170.0045-0.0078-0.01180.04840.155-0.20520.1625-0.0226-0.07140.3042-0.25790.00030.4416-0.1129-0.00590.31610.00690.4961-20.834635.687642.8742
290.36540.29120.18850.17660.1310.11530.00890.09640.0354-0.06080.02990.0793-0.21760.01080.00280.25320.055-0.03240.2945-0.01240.2426-17.315569.705816.8179
300.31720.29530.04870.32860.15430.06530.08390.1382-0.14790.0342-0.06210.0051-0.0115-0.06150.00230.17490.0515-0.04520.2688-0.05840.2547-22.687153.679514.5077
310.13180.15390.03230.11250.0194-0.01160.05060.3260.0422-0.10870.0060.10050.1254-0.1350.00450.2589-0.0038-0.04660.421-0.11120.3726-29.973648.220511.5765
320.0058-0.0133-0.00180.02280.0015-0.00030.1502-0.24820.07980.0458-0.0248-0.120.0343-0.04220.00440.34770.075-0.04820.3977-0.0140.31466.618359.885454.5889
330.0064-0.02220.0230.0194-0.00660.01250.1784-0.06350.1576-0.0084-0.0654-0.09220.0482-0.2554-00.2998-0.0045-0.00340.272-0.01430.2079-6.485276.05842.8756
340.17080.0840.03350.05350.04350.03260.0417-0.05410.0070.12230.00830.0051-0.06030.176900.3066-0.01080.02240.26180.01280.1587-3.577182.630152.2853
350.321-0.04170.1294-0.0009-0.01910.0543-0.0068-0.18180.07040.0197-0.0366-0.0489-0.0764-0.11860.00150.3046-0.04640.00270.14830.05760.19790.979980.015361.5319
360.0173-0.01860.00190.0121-0.0011-0.0011-0.0274-0.0648-0.14960.0298-0.03040.04970.03320.115-0.00010.2664-0.020.02670.28940.00110.16086.294780.756454.9545
370.12240.00120.05910.01030.01610.03340.0170.01160.0978-0.1981-0.0543-0.00920.15530.09790.00010.38760.0333-0.04670.33840.00810.301814.121972.641144.2915
380.0374-0.01480.05530.0409-0.0060.053-0.10770.07450.0012-0.0415-0.06220.0389-0.17260.1747-0.00010.3207-0.01390.05360.3863-0.0160.380525.762595.280140.4778
390.01590.0227-0.02470.0019-0.03220.05920.2246-0.0636-0.0391-0.1702-0.11890.1804-0.15120.16390.00010.3146-0.0279-0.04370.23090.04690.259913.528987.498948.0285
400.63850.0286-0.06520.1651-0.13230.63020.2904-0.15990.19950.0501-0.26880.0932-0.30080.2410.04350.2438-0.0998-0.030.24030.00950.222619.834890.99654.9473
410.23160.1664-0.14290.104-0.08180.12760.01650.1079-0.047-0.1002-0.05030.00180.3084-0.0542-0.00010.30470.042-0.00920.2356-0.02130.16912.345771.356816.3673
420.00590.0102-0.00390.00950.0070.0036-0.1310.0686-0.09980.0207-0.1371-0.12430.17030.04430.00010.47460.05220.00910.44230.00620.421916.125270.96657.1158
430.12050.0244-0.06330.1252-0.04840.0516-0.0318-0.0528-0.1309-0.10650.01010.01290.0954-0.1326-0.09240.26750.0737-0.01230.1940.0196-0.008310.817678.992911.3314
440.04-0.00330.02040.1397-0.13990.1747-0.07390.0514-0.0165-0.1020.038-0.00220.00110.08-00.2999-0.02590.06220.28130.00420.279210.017292.987324.8255
450.05090.02430.0430.0952-0.02060.01380.15370.05570.0309-0.13630.0705-0.1583-0.2599-0.06270.00050.37380.00910.04010.3123-0.02240.302715.55893.021522.8906
460.08430.14030.13140.20270.17710.1965-0.13580.15470.1358-0.44240.3991-0.0423-0.19090.25370.00020.3057-0.02360.08620.31190.02880.293319.240397.299114.5139
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 106 )A9 - 106
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 247 )A107 - 247
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 335 )A248 - 335
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 28 )B9 - 28
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 88 )B29 - 88
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 106 )B89 - 106
7X-RAY DIFFRACTION7chain 'B' and (resid 107 through 131 )B107 - 131
8X-RAY DIFFRACTION8chain 'B' and (resid 132 through 212 )B132 - 212
9X-RAY DIFFRACTION9chain 'B' and (resid 213 through 247 )B213 - 247
10X-RAY DIFFRACTION10chain 'B' and (resid 248 through 290 )B248 - 290
11X-RAY DIFFRACTION11chain 'B' and (resid 291 through 335 )B291 - 335
12X-RAY DIFFRACTION12chain 'C' and (resid 9 through 131 )C9 - 131
13X-RAY DIFFRACTION13chain 'C' and (resid 132 through 335 )C132 - 335
14X-RAY DIFFRACTION14chain 'D' and (resid 9 through 28 )D9 - 28
15X-RAY DIFFRACTION15chain 'D' and (resid 29 through 48 )D29 - 48
16X-RAY DIFFRACTION16chain 'D' and (resid 49 through 88 )D49 - 88
17X-RAY DIFFRACTION17chain 'D' and (resid 89 through 106 )D89 - 106
18X-RAY DIFFRACTION18chain 'D' and (resid 107 through 179 )D107 - 179
19X-RAY DIFFRACTION19chain 'D' and (resid 180 through 212 )D180 - 212
20X-RAY DIFFRACTION20chain 'D' and (resid 213 through 231 )D213 - 231
21X-RAY DIFFRACTION21chain 'D' and (resid 232 through 247 )D232 - 247
22X-RAY DIFFRACTION22chain 'D' and (resid 248 through 290 )D248 - 290
23X-RAY DIFFRACTION23chain 'D' and (resid 291 through 335 )D291 - 335
24X-RAY DIFFRACTION24chain 'E' and (resid 9 through 88 )E9 - 88
25X-RAY DIFFRACTION25chain 'E' and (resid 89 through 122 )E89 - 122
26X-RAY DIFFRACTION26chain 'E' and (resid 123 through 155 )E123 - 155
27X-RAY DIFFRACTION27chain 'E' and (resid 156 through 247 )E156 - 247
28X-RAY DIFFRACTION28chain 'E' and (resid 248 through 335 )E248 - 335
29X-RAY DIFFRACTION29chain 'F' and (resid 9 through 106 )F9 - 106
30X-RAY DIFFRACTION30chain 'F' and (resid 107 through 247 )F107 - 247
31X-RAY DIFFRACTION31chain 'F' and (resid 248 through 335 )F248 - 335
32X-RAY DIFFRACTION32chain 'G' and (resid 9 through 28 )G9 - 28
33X-RAY DIFFRACTION33chain 'G' and (resid 29 through 88 )G29 - 88
34X-RAY DIFFRACTION34chain 'G' and (resid 89 through 131 )G89 - 131
35X-RAY DIFFRACTION35chain 'G' and (resid 132 through 148 )G132 - 148
36X-RAY DIFFRACTION36chain 'G' and (resid 149 through 170 )G149 - 170
37X-RAY DIFFRACTION37chain 'G' and (resid 171 through 212 )G171 - 212
38X-RAY DIFFRACTION38chain 'G' and (resid 213 through 247 )G213 - 247
39X-RAY DIFFRACTION39chain 'G' and (resid 248 through 290 )G248 - 290
40X-RAY DIFFRACTION40chain 'G' and (resid 291 through 335 )G291 - 335
41X-RAY DIFFRACTION41chain 'H' and (resid 9 through 88 )H9 - 88
42X-RAY DIFFRACTION42chain 'H' and (resid 89 through 106 )H89 - 106
43X-RAY DIFFRACTION43chain 'H' and (resid 107 through 179 )H107 - 179
44X-RAY DIFFRACTION44chain 'H' and (resid 180 through 231 )H180 - 231
45X-RAY DIFFRACTION45chain 'H' and (resid 232 through 290 )H232 - 290
46X-RAY DIFFRACTION46chain 'H' and (resid 291 through 335 )H291 - 335

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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