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- PDB-6bht: HIV-1 CA hexamer in complex with IP6, orthorhombic crystal form -

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データを開く


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基本情報

登録情報
データベース: PDB / ID: 6bht
タイトルHIV-1 CA hexamer in complex with IP6, orthorhombic crystal form
要素Capsid protein p24
キーワードVIRAL PROTEIN / assembly / co-factor
機能・相同性
機能・相同性情報


viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane
類似検索 - 分子機能
Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) ...Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
INOSITOL HEXAKISPHOSPHATE / Gag polyprotein
類似検索 - 構成要素
生物種Human immunodeficiency virus type 1 (ヒト免疫不全ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.689 Å
データ登録者Zadrozny, K. / Wagner, J.M. / Ganser-Pornillos, B.K. / Pornillos, O.
資金援助 米国, 2件
組織認可番号
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI129678 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM103297 米国
引用ジャーナル: Nature / : 2018
タイトル: Inositol phosphates are assembly co-factors for HIV-1.
著者: Dick, R.A. / Zadrozny, K.K. / Xu, C. / Schur, F.K.M. / Lyddon, T.D. / Ricana, C.L. / Wagner, J.M. / Perilla, J.R. / Ganser-Pornillos, B.K. / Johnson, M.C. / Pornillos, O. / Vogt, V.M.
履歴
登録2017年10月31日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年8月1日Provider: repository / タイプ: Initial release
改定 1.12018年8月15日Group: Data collection / Database references / Source and taxonomy
カテゴリ: citation / citation_author / entity_src_gen
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity_src_gen.pdbx_gene_src_scientific_name
改定 1.22018年9月5日Group: Data collection / Database references / Source and taxonomy
カテゴリ: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name
改定 1.32019年2月20日Group: Author supporting evidence / Data collection / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52020年10月14日Group: Structure summary / カテゴリ: chem_comp / Item: _chem_comp.pdbx_synonyms
改定 1.62023年10月4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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24
K: Capsid protein p24
L: Capsid protein p24
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)308,17516
ポリマ-305,53512
非ポリマー2,6404
3,117173
1
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)154,0888
ポリマ-152,7686
非ポリマー1,3202
1086
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area16490 Å2
ΔGint-110 kcal/mol
Surface area60240 Å2
手法PISA
2
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24
K: Capsid protein p24
L: Capsid protein p24
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)154,0888
ポリマ-152,7686
非ポリマー1,3202
1086
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area15260 Å2
ΔGint-124 kcal/mol
Surface area59370 Å2
手法PISA
単位格子
Length a, b, c (Å)135.317, 137.173, 209.354
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

#1: タンパク質
Capsid protein p24 / Pr55Gag


分子量: 25461.271 Da / 分子数: 12 / 変異: A146C, E177C, W316A, M317A / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) (ヒト免疫不全ウイルス)
: NEW YORK-5 ISOLATE / 遺伝子: gag / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P12493
#2: 化合物
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / フィチン酸


分子量: 660.035 Da / 分子数: 4 / 由来タイプ: 合成 / : C6H18O24P6
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 173 / 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: 3.18 Å3/Da / 溶媒含有率: 61.32 %
結晶化温度: 290 K / 手法: 蒸気拡散法 / pH: 8.2 / 詳細: 8% PEG 8000, 0.1M Tris

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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: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: MARRESEARCH / 検出器: CCD / 日付: 2017年8月1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: 2.689→50 Å / Num. obs: 108358 / % possible obs: 99.3 % / 冗長度: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1
反射 シェル解像度: 2.689→2.74 Å / Rmerge(I) obs: 0.79

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575: ???)精密化
HKL-2000データ削減
HKL-2000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: 3H4E
解像度: 2.689→39.77 Å / SU ML: 0.32 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 27.06 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2546 2000 2.09 %
Rwork0.2267 --
obs0.2273 95906 88.23 %
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
精密化ステップサイクル: LAST / 解像度: 2.689→39.77 Å
タンパク質核酸リガンド溶媒全体
原子数19441 0 144 173 19758
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00320039
X-RAY DIFFRACTIONf_angle_d0.62827323
X-RAY DIFFRACTIONf_dihedral_angle_d8.89412223
X-RAY DIFFRACTIONf_chiral_restr0.3563110
X-RAY DIFFRACTIONf_plane_restr0.0043522
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6885-2.75580.3681400.30942545X-RAY DIFFRACTION34
2.7558-2.83030.35551130.30563840X-RAY DIFFRACTION52
2.8303-2.91350.2966860.29315362X-RAY DIFFRACTION71
2.9135-3.00750.36661400.29916672X-RAY DIFFRACTION88
3.0075-3.1150.33711790.28537342X-RAY DIFFRACTION98
3.115-3.23960.29631140.27087533X-RAY DIFFRACTION99
3.2396-3.3870.30852240.2677498X-RAY DIFFRACTION100
3.387-3.56550.30551120.25447601X-RAY DIFFRACTION100
3.5655-3.78870.28312130.23837468X-RAY DIFFRACTION100
3.7887-4.0810.26031230.21577593X-RAY DIFFRACTION99
4.081-4.49110.2141610.18997537X-RAY DIFFRACTION99
4.4911-5.13980.1931710.17677558X-RAY DIFFRACTION99
5.1398-6.47110.20281120.21557683X-RAY DIFFRACTION99
6.4711-39.77440.19092120.17657674X-RAY DIFFRACTION97
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)
10.01110.01360.00110.0492-0.01070.0045-0.0459-0.0432-0.05530.03710.00340.03340.0326-0.0201-0.01120.2348-0.07350.06790.29880.01370.2199-20.3708-64.8107-33.0234
20.00680.0001-0.00220.0065-0.0030.0080.03570.00770.1320.041-0.01370.0085-0.02750.0840.03470.1398-0.0361-0.020.17780.04120.194-0.6821-55.2546-30.5478
30.0198-0.0076-0.03920.0093-0.01890.16610.01010.01620.0065-0.0904-0.0075-0.1295-0.10560.19050.22120.1272-0.10280.1280.05130.05610.0396-0.7223-62.7365-44.267
40.0397-0.0016-0.01240.0246-0.01030.0087-0.06110.0431-0.05830.0106-0.01080.0194-0.0345-0.0795-0.1270.2880.00310.08250.2104-0.13760.2363-13.0143-75.9068-53.1286
50.06960.02560.00680.00930.00020.074-0.0466-0.0223-0.1356-0.0445-0.09130.17010.0319-0.027-0.1250.2223-0.01650.00950.10190.01040.2265-15.2358-70.1801-44.9961
60.0839-0.0616-0.14110.1190.21280.39390.0545-0.0396-0.03570.01720.06010.03190.00710.08880.25290.1509-0.0007-0.03020.05070.00870.06183.3121-65.7152-38.936
70.02010.0174-0.01790.0139-0.01580.0173-0.0129-0.0591-0.00770.0058-0.0198-0.0633-0.00220.0302-0.03480.1823-0.13180.03530.8039-0.01270.431525.1963-58.209-22.1273
80.06330.023-0.07810.0373-0.02290.1123-0.0221-0.0315-0.0202-0.0243-0.0298-0.02620.04140.0681-0.07410.17330.10330.01210.6128-0.05760.161918.0811-61.8925-20.9253
90.0517-0.005-0.0050.00110.00080.01360.014-0.0018-0.03150.0146-0.0677-0.13160.01790.1235-0.0810.45960.3032-0.1141.12720.16670.534123.8285-68.6316-13.8698
100.05090.0062-0.01230.037-0.00440.0197-0.0135-0.0181-0.00190.04340.03020.05950.0156-0.05790.01580.2852-0.07510.13120.4365-0.01810.1885-18.1856-68.702-21.4124
110.0276-0.00480.01220.01030.01440.0340.02740.00420.0229-0.00540.0368-0.0026-0.00090.06780.02920.2253-0.0503-0.04390.2657-0.05840.185-2.0325-55.1898-17.2896
120.0564-0.0418-0.01070.03620.02320.0592-0.0797-0.020.01110.0110.0256-0.02840.07610.0577-0.15730.16790.04910.05840.2137-0.04280.0639-1.2516-63.6645-15.0272
130.0428-0.01780.00380.09970.02270.01530.04530.0314-0.03080.09140.0442-0.07610.19240.10250.0650.42340.1946-0.01760.3417-0.02710.2247.9716-76.0378-13.6875
140.1081-0.02330.00910.0296-0.03160.03970.1758-0.0331-0.11770.0083-0.12850.05880.069-0.12960.07650.4962-0.1093-0.0010.2299-0.07220.2314-7.0003-84.2843-20.4781
150.0676-0.04590.0770.1188-0.10860.1230.054-0.0840.0450.03230.0251-0.0607-0.0060.00720.15210.34960.01220.05630.2953-0.08660.02082.9231-70.0275-9.1485
160.00610.00470.00080.00370.00160.00110.06840.01380.09660.02150.0087-0.02330.00010.068-0.00040.4427-0.0130.08520.9006-0.23540.48512.9006-51.85859.3586
170.00110.00280.00250.00920.00790.00640.02130.00490.008-0.0823-0.0243-0.00790.04140.0405-0.01850.28170.0846-0.01270.3775-0.11840.1295.1916-53.63087.6403
180.03150.00710.01280.01370.0090.00970.012-0.0275-0.0022-0.09320.0617-0.00530.07790.01710.010.5763-0.0654-0.02060.788-0.01380.19627.8042-59.631914.3138
190.0951-0.0256-0.02340.04090.01690.09670.0712-0.03140.0155-0.05020.038-0.0506-0.05120.07520.13410.2783-0.04210.02850.5804-0.06840.18782.0603-51.475822.0304
200.03120.0098-0.01870.073-0.06570.06660.05230.0225-0.04070.12650.0871-0.0707-0.07020.04610.2750.17310.0157-0.020.2518-0.1020.123-16.7101-53.8542-7.032
210.0671-0.0484-0.03810.17970.17110.17180.0372-0.0526-0.08740.1422-0.06180.04730.2185-0.0137-0.03750.22070.0361-0.01010.2521-0.0150.093-17.536-66.37765.7527
220.06590.0525-0.00030.1154-0.02110.0072-0.0863-0.0151-0.01930.15990.01390.0510.0268-0.0243-0.22320.23250.04880.01720.2083-0.15690.2344-15.6618-53.55038.3125
230.0517-0.03310.0590.05320.00060.1108-0.0664-0.00760.08030.0636-0.0188-0.0185-0.09110.0592-0.2840.3548-0.0576-0.07670.1548-0.11130.1668-13.7988-28.14289.6111
240.03020.01930.00890.05370.02950.0160.0626-0.0024-0.0017-0.0017-0.0111-0.01150.00450.01690.07850.44440.0694-0.0020.4674-0.19620.2429-21.8667-31.437817.0444
250.0025-0.00680.00250.0158-0.00550.0023-0.0178-0.02810.05170.0462-0.0084-0.0059-0.0528-0.0431-0.0380.51890.1631-0.1470.4559-0.31960.4881-24.1086-17.818410.4622
260.0025-0.0003-0.00230.00520.00310.0031-0.0394-0.00310.01020.04850.04850.0125-0.0331-0.020800.26710.039-0.00390.3815-0.12640.3984-32.6352-54.97-14.6736
270.0385-0.00610.02920.0144-0.01960.0676-0.05120.020.0128-0.03260.0402-0.04960.01230.041-0.07520.26340.0162-0.03970.071-0.03480.1189-21.5949-36.1682-11.8656
280.0650.00410.00490.0228-0.03170.0581-0.0207-0.05590.10990.2194-0.03820.1971-0.0466-0.0267-0.18430.21610.05170.04120.2619-0.13890.2184-31.1991-37.39630.3184
290.1098-0.0019-0.02010.0153-0.00050.1078-0.02410.0217-0.0430.0449-0.03620.10580.0651-0.0331-0.05310.3331-0.0470.24550.3805-0.06090.384-42.6948-46.75153.7579
300.00720.0133-0.00330.0269-0.00280.0076-0.04460.01550.00730.0074-0.00270.07080.0634-0.0573-0.00080.2279-0.0670.10660.1916-0.06990.3477-41.734-51.7164-4.7704
310.00560.00930.01270.02110.02050.1298-0.05440.0236-0.0270.05010.04940.0507-0.13660.01260.00120.21750.0683-0.03110.228-0.01450.2552-32.8529-32.3341-4.6823
32-0.00040.00030.00030.001-00.0002-0.0073-0.01220.04550.02830.0755-0.0901-0.03880.05130.03170.8006-0.1102-0.13870.2718-0.13820.5489-21.2887-9.1877-15.7981
330.0135-0.0035-0.01150.01110.00210.0081-0.0492-0.02440.01740.04450.00250.0217-0.0215-0.0097-0.09040.40630.1045-0.04840.0736-0.07730.3016-25.2224-15.6004-19.0219
340.04770.0060.01490.00130.00130.00810.04-0.1130.0753-0.02580.1086-0.0889-0.1126-0.03460.00091.06880.2197-0.01620.35370.00650.6646-29.9079-6.1924-22.5514
350.0307-0.0083-0.0020.04450.02460.0140.0244-0.0030.0384-0.02030.04640.0144-0.0219-0.02890.02220.5090.1836-0.04310.23330.03550.5454-30.8979-9.8308-31.2211
360.06250.0214-0.02160.0179-0.03070.07780.0499-0.03160.00560.01030.0655-0.0278-0.00660.04480.18290.2473-0.0764-0.13540.0534-0.03480.2187-25.899-40.0091-27.9961
370.09470.0158-0.19480.0699-0.05620.40270.03870.08130.10290.01650.07030.1269-0.102-0.17890.27310.130.0469-0.06370.1131-0.02030.2499-35.1644-28.0766-27.412
380.04430.03420.00720.02690.01640.0623-0.00670.0249-0.0355-0.05850.0970.11190.0375-0.10420.09070.17-0.1021-00.32430.14550.4729-46.7742-38.2966-26.8487
390.1398-0.003-0.07380.05020.03390.1120.1529-0.00010.0722-0.00740.1219-0.05870.1226-0.14020.26260.1947-0.0247-0.06750.20630.03890.2533-32.3827-27.9467-34.3693
400.0205-0.0034-0.00380.03980.02290.0123-0.07860.02880.0323-0.09650.00350.0409-0.0447-0.0387-0.36150.3003-0.1149-0.12470.04470.13560.3496-13.5473-21.6385-50.3019
410.020.0382-0.00630.0746-0.00470.047-0.0570.03240.0175-0.0559-0.0279-0.0578-0.00170.0253-0.08030.5245-0.14440.03990.23160.07720.2102-7.2702-26.4141-61.8859
420.1004-0.02380.01670.05060.00370.0042-0.00620.0049-0.0272-0.0127-0.00180.01390.0324-0.02790.08460.3262-0.079-0.01430.0708-0.07270.3129-28.3205-56.1002-34.4732
430.0034-0.0067-0.00330.01460.0070.0074-0.0019-0.0150.03220.0115-0.0024-0.0299-0.04960.0203-0.00840.2195-0.0965-0.02570.0689-0.09620.242-11.9488-41.4522-34.7239
440.0153-0.0124-0.00890.02460.00410.0384-0.01610.01120.0687-0.0318-0.0047-0.0544-0.09210.0453-0.12780.1901-0.1042-0.066-0.00170.02960.1899-15.5661-43.8333-42.4527
450.0083-0.0093-0.00610.02210.0020.00750.03490.07110.0402-0.1030.05080.06690.0123-0.03930.08120.3199-0.1091-0.10050.12390.07350.1784-20.1283-40.1854-56.7771
460.0226-0.00250.03520.0585-0.02370.0607-0.00430.0306-0.0305-0.01510.0340.0308-0.01-0.00580.02920.28-0.1619-0.23630.38710.03350.4485-36.9116-50.6708-57.4396
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480.00060.0005-0.00180.0242-0.05030.1024-0.04140.03220.0297-0.0007-0.03680.0148-0.04660.0263-0.11290.2273-0.087-0.06950.0535-0.02780.2216-14.2961-45.0866-51.8774
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500.00060.0007-0.0005-0.0001-0.00090.0001-0.01550.03010.0337-0.06650.0289-0.0077-0.04450.05370.04320.2314-0.1560.02560.21380.04540.12968.8123-48.0856-48.5768
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540.01370.01050.00360.0237-0.00510.0042-0.0070.007-0.01720.0127-0.01610.02250.0289-0.02440.01410.2068-0.13820.16920.4245-0.30410.4704-61.7843-88.7116-18.7877
550.02-0.0248-0.02740.05330.02860.03570.01770.0015-0.00460.00320.0070.006-0.01050.00740.1580.4078-0.19220.26520.4077-0.2930.4783-57.6658-92.0075-10.2443
560.01760.00780.02140.00420.01290.11770.04180.0314-0.02980.1148-0.02830.07920.02420.02450.06780.5252-0.32640.46430.7148-0.47030.7026-62.4396-80.2678-3.2482
570.0789-0.033-0.06710.09280.01890.0813-0.01050.0302-0.00490.0114-0.01170.00610.0134-0.0602-0.12380.5155-0.2420.2850.5255-0.29860.5719-51.9876-63.97323.358
580.0256-0.00850.02140.0029-0.00720.0182-0.00660.0015-0.01260.0223-0.05250.04380.0039-0.0465-0.29740.4028-0.23770.22880.5437-0.30960.4893-51.4907-68.2582-5.726
590.01390.00690.00770.0352-0.00840.0104-0.03970.0022-0.03610.0568-0.00150.02680.0643-0.0088-0.08560.5076-0.25640.27090.5222-0.32470.5073-58.7765-86.3823-1.4696
600.05420.0316-0.00190.0306-0.0070.0356-0.002-0.0449-0.056-0.01460.0029-0.01190.0573-0.02970.04290.8584-0.29460.41770.77290.02020.8933-62.8273-114.155-3.2132
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620.00450.0013-0.0030.0004-0.00080.0018-0.0482-0.036-0.03650.0228-0.0449-0.01450.03360.0323-0.00021.0991-0.03490.35320.86660.1150.9805-53.4333-117.10921.7237
630.00020.0005-0.0010.0008-0.00180.0029-0.0063-0.01120.0051-0.02310.006-0.0560.01310.00701.0796-0.0090.24030.80950.02760.663-45.2038-118.5518-3.7516
640.0933-0.00250.01590.0539-0.02960.01770.03720.03210.0641-0.0175-0.0436-0.03440.01430.0407-0.03890.3994-0.22910.15040.7051-0.17660.3533-38.7013-81.3608-20.2881
650.0151-0.0098-0.01770.02290.00890.0197-0.0154-0.0064-0.00670.0091-0.00590.03010.02-0.04080.01840.3424-0.12260.20610.4021-0.22620.4309-52.1325-98.0122-22.3094
660.00790.00280.01340.00720.00930.03280.04780.00120.01390.01810.02340.0041-0.00340.04550.33260.4872-0.20590.23550.4553-0.24160.2655-44.9145-98.8116-17.2575
670.02910.01570.01130.0578-0.00480.0057-0.0432-0.07010.00790.13280.072-0.05450.08720.0142-0.01420.8409-0.12470.12490.6991-0.14950.3094-38.4856-104.7129-4.6848
680.0480.02020.05210.3557-0.04150.0691-0.07980.0748-0.01860.0714-0.05930.0147-0.05030.007-0.07680.7078-0.18720.0850.4787-0.14150.272-27.7055-88.50790.2342
690.0044-0.00840.00540.0177-0.01010.00640.00120.0227-0.0026-0.0091-0.04970.02170.0230.0032-0.13150.4787-0.16640.21370.6609-0.18910.3483-33.3544-86.3992-7.8842
700.0377-0.00940.04380.0025-0.01080.05070.06620.00510.0342-0.00230.0215-0.05370.12090.04070.14670.6211-0.03430.15380.5427-0.19250.3077-38.4349-104.7599-13.6913
710.0047-0.0003-0.00390.0087-0.00190.0035-0.0107-0.0008-0.06470.00930.04920.0130.0318-0.02090.00281.0273-0.09130.05730.4852-0.15550.7099-45.4888-126.4763-30.2821
720.01480.01560.010.03490.03830.0486-0.0128-0.008-0.05230.00510.00790.03150.03960.00590.03980.53540.06610.14460.3839-0.21280.3469-41.4921-119.4076-31.3968
730.0026-0-0.00190.0044-0.00510.0066-0.0175-0.0866-0.0104-0.0130.0038-0.03460.0987-0.0286-00.98390.09320.04950.489-0.09010.6763-34.724-123.8199-30.2839
7400.00030.00050.01180.01230.01620.00510.00340.00590.0178-0.0014-0.02790.05130.0013-0.0130.89090.11480.17380.5801-0.36310.7875-33.1169-130.4484-41.5122
750.00390.001-0.01010.0007-0.00370.0267-0.04320.011-0.0099-0.03060.0156-0.04160.006-0.008-0.00350.82520.07720.16480.4941-0.20510.5534-36.1989-122.5599-44.4283
760.0805-0.00670.00190.00350.01130.04480.009-0.00420.01890.0320.0167-0.0162-0.00380.0302-0.03420.4269-0.24610.10060.726-0.20850.3299-34.0996-83.1828-31.3295
77-0.00010.00190.00090.02710.01340.00680.0053-0.02490.0080.0066-0.02480.04980.0487-0.0153-0.00560.2793-0.12290.07310.3156-0.19740.2649-47.9153-100.1294-35.7541
780.0363-0.0715-0.03080.18920.01980.06030.0584-0.06850.0411-0.1101-0.028-0.0057-0.00860.09850.19650.2492-0.05210.03490.4343-0.21410.1617-39.4823-100.3939-37.6304
790.0212-0.01670.0070.1323-0.00780.0021-0.0595-0.02830.02990.07240.0598-0.14810.05840.0045-0.10010.39660.08540.02430.3531-0.20880.2965-26.6887-108.9186-38.5088
800.0206-0.05280.0060.1363-0.01060.0074-0.15350.02370.07560.0726-0.0596-0.0696-0.1014-0.1158-0.11360.3767-0.0703-0.05960.4077-0.15880.3992-14.1725-96.0235-30.9644
810.01150.00740.02040.04640.02350.0361-0.0033-0.07270.03790.01460.0493-0.0442-0.02650.03590.05910.3632-0.11170.02840.474-0.16010.1702-23.3212-91.7434-30.9076
820.08190.01580.02190.02790.0350.04310.00340.0423-0.038-0.0332-0.04280.0429-0.03140.0456-0.12080.2885-0.0115-0.04920.4146-0.13220.1158-32.8121-104.4496-43.2801
830.00160.0260.00150.29530.01630.00080.03550.0064-0.0446-0.10080.03930.10010.07940.00880.12830.46360.0634-0.18110.2685-0.12010.2893-50.3122-110.5688-61.5492
840.01240.00450.00190.02360.00070.0203-0.00860.0224-0.0186-0.04950.01-0.04350.02270.01230.00040.66120.1142-0.10250.4609-0.01610.4396-41.1998-109.567-66.2642
850.00520.0078-0.02260.0503-0.09810.20320.05630.0026-0.0332-0.01180.036-0.00340.0562-0.0410.02280.8405-0.1519-0.17450.5005-0.13680.4781-51.2722-110.1269-76.0831
860.0029-0.00860.00530.0257-0.0150.01020.0044-0.00270.0209-0.01480.00570.0502-0.04510.02640.01230.6271-0.0477-0.1910.6974-0.21680.5213-51.8459-100.7981-73.0197
870.00350.00180.00060.0028-0.00230.00460.014-0.00350.0188-0.00730.0083-0.0096-0.00770.01750.01460.1906-0.04250.02650.3956-0.28780.4855-38.7487-78.5474-41.8397
880.0881-0.03410.00510.0137-0.00240.0010.0398-0.0307-0.02040.017-0.01380.03840.01930.00910.03820.1418-0.0366-0.06360.3553-0.17750.4157-53.7096-92.087-45.3609
890.021-0.0124-0.00270.02450.00370.00220.0102-0.0024-0.01220.00050.00780.00220.00490.02160.10870.0591-0.0288-0.00560.1675-0.29110.2282-49.0695-88.5947-52.0487
900.03380.03270.05770.03490.06050.1066-0.0510.0889-0.0447-0.0614-0.00470.0642-0.0688-0.0054-0.20440.28920.0316-0.09210.326-0.24240.2428-41.9706-90.2598-65.6886
910.0085-0.00480.00640.0588-0.03450.0213-0.07420.0917-0.01220.053-0.0452-0.0075-0.07460.0448-0.0160.188-0.0167-0.03310.3648-0.12220.2985-28.681-82.189-61.5299
920.0511-0.03050.00160.0197-0.00490.03150.0242-0.0210.0513-0.0596-0.02730.0051-0.0614-0.0171-0.01650.21970.0150.01340.3085-0.20540.3268-31.4012-77.386-52.6674
930.02170.00570.00790.0107-0.02440.0804-0.04090.07410.0063-0.0199-0.08850.0486-0.0109-0.0386-0.24920.11880.0744-0.1220.2927-0.17560.3407-48.1028-85.6555-61.312
940.00980.0221-0.01010.0706-0.06090.07740.0763-0.0251-0.00050.05320.0106-0.03030.107-0.02580.18840.2353-0.0872-0.07030.3775-0.24850.4785-74.8867-91.7683-64.0358
950.00160.0087-0.00620.0541-0.0410.032-0.00350.0074-0.0254-0.03610.0085-0.00580.0273-0.05570.08420.13710.01520.03910.4353-0.2030.3107-72.9473-85.3355-60.4963
960.00210.0005-0.00230.0003-0.00080.00220.0230.02060.0239-0.0828-0.06380.0259-0.04970.0064-00.55810.1247-0.18020.5412-0.0920.5033-71.5369-80.0324-69.9481
970.0112-0.0070.00470.0105-0.00130.00230.0035-0.02110.0127-0.0052-0.00320.02510.0001-0.03250.0270.4107-0.0379-0.21370.8704-0.28440.8429-87.8318-83.4229-65.4351
980.00580.00550.00190.0099-0.00410.0132-0.023-0.01150.032-0.0182-0.0759-0.0077-0.0127-0.0088-0.0030.46340.1946-0.20480.8052-0.2570.9681-82.6509-75.0639-59.78
990.04480.02530.01480.08950.00840.0062-0.00640.0189-0.01730.0455-0.04780.0261-0.0178-0.0588-0.05140.31870.0141-0.14410.4125-0.27080.4532-47.2278-68.8317-39.3018
1000.1242-0.0531-0.00590.07320.05270.05020.01960.0023-0.0330.0049-0.00440.0160.00660.01060.05040.1349-0.03280.00810.3514-0.31280.4969-63.3986-82.9381-41.8399
1010.02920.00130.01310.00040.00260.00680.0178-0.0350.03280.0231-0.05190.0710.0148-0.05470.01420.1656-0.0409-0.01670.4115-0.42770.5338-63.9592-75.0768-45.7434
1020.0716-0.0236-0.01510.00750.00460.0502-0.06640.01130.0116-0.0015-0.056-0.0064-0.0427-0.0591-0.30840.13830.1104-0.13210.2763-0.20530.5965-68.1631-66.425-57.9269
1030.09350.05190.07890.1120.03050.0667-0.02780.04260.0256-0.0154-0.0729-0.0035-0.0287-0.0339-0.16630.13460.0346-0.06350.1915-0.14940.5531-52.5944-60.11-53.4631
1040.0157-0.0033-0.01770.00740.00890.02350.00830.01610.03010.0137-0.01460.0259-0.0066-0.07750.10780.18280.08760.09060.3749-0.30420.753-69.5566-68.2358-49.0537
1050.04040.03180.03260.02490.02130.07530.05590.00420.004-0.00130.03-0.01260.0166-0.02610.02680.3888-0.14020.12620.9305-0.27621.007-93.2793-77.979-38.2034
1060.0148-0.00180.00660.0247-0.0420.07010.0520.02110.01120.00750.02450.0329-0.0415-0.04840.12830.22560.04880.08930.575-0.32880.7791-87.1275-74.8946-34.2472
1070.00380.0011-0.0016-0-0.00030.0005-0.0129-0.00960.0025-0.0328-0.00220.0458-0.0393-0.06890.00010.81960.32810.20751.0131-0.1681.0815-95.4436-69.0505-35.421
1080.0395-0.0016-0.01320.0004-0.00010.0060.01110.02070.0188-0.00830.0014-0.0054-0.0231-0.0245-0.0090.48460.19660.33730.9527-0.1340.918-99.5348-67.8665-26.3129
1090.0328-0.0169-0.03150.00880.01620.0299-0.00820.00190.0110.01970.02060.00750.0041-0.00240.02460.50010.02140.32981.0723-0.2941.0689-91.5779-70.7583-22.2105
1100.0252-0.00850.02540.05980.01070.0439-0.06510.0783-0.12260.0484-0.09980.1563-0.0087-0.1337-0.89920.1399-0.20440.13680.6087-0.45670.7793-67.9743-67.3838-26.2069
1110.15620.0090.15150.4265-0.3360.4287-0.13150.00590.08050.0488-0.05260.0136-0.08190.0647-0.46730.3202-0.20360.1590.4588-0.34570.6646-67.6993-62.847-22.0457
1120.05350.03690.01330.0535-0.00690.01010.0174-0.0325-0.06570.12660.00170.07240.0393-0.10180.19180.7764-0.31230.53670.8222-0.35961.0577-81.3026-88.7743-0.3499
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 104 )
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 125 )
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 145 )
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 160 )
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 176 )
9X-RAY DIFFRACTION9chain 'A' and (resid 177 through 221 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 16 )
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 30 )
12X-RAY DIFFRACTION12chain 'B' and (resid 31 through 62 )
13X-RAY DIFFRACTION13chain 'B' and (resid 63 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 125 )
15X-RAY DIFFRACTION15chain 'B' and (resid 126 through 145 )
16X-RAY DIFFRACTION16chain 'B' and (resid 146 through 160 )
17X-RAY DIFFRACTION17chain 'B' and (resid 161 through 175 )
18X-RAY DIFFRACTION18chain 'B' and (resid 176 through 195 )
19X-RAY DIFFRACTION19chain 'B' and (resid 196 through 219 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 43 )
21X-RAY DIFFRACTION21chain 'C' and (resid 44 through 125 )
22X-RAY DIFFRACTION22chain 'C' and (resid 126 through 145 )
23X-RAY DIFFRACTION23chain 'C' and (resid 146 through 175 )
24X-RAY DIFFRACTION24chain 'C' and (resid 176 through 192 )
25X-RAY DIFFRACTION25chain 'C' and (resid 193 through 219 )
26X-RAY DIFFRACTION26chain 'D' and (resid 1 through 16 )
27X-RAY DIFFRACTION27chain 'D' and (resid 17 through 43 )
28X-RAY DIFFRACTION28chain 'D' and (resid 44 through 83 )
29X-RAY DIFFRACTION29chain 'D' and (resid 84 through 110 )
30X-RAY DIFFRACTION30chain 'D' and (resid 111 through 125 )
31X-RAY DIFFRACTION31chain 'D' and (resid 126 through 145 )
32X-RAY DIFFRACTION32chain 'D' and (resid 146 through 160 )
33X-RAY DIFFRACTION33chain 'D' and (resid 161 through 176 )
34X-RAY DIFFRACTION34chain 'D' and (resid 177 through 205 )
35X-RAY DIFFRACTION35chain 'D' and (resid 206 through 219 )
36X-RAY DIFFRACTION36chain 'E' and (resid 1 through 43 )
37X-RAY DIFFRACTION37chain 'E' and (resid 44 through 83 )
38X-RAY DIFFRACTION38chain 'E' and (resid 84 through 125 )
39X-RAY DIFFRACTION39chain 'E' and (resid 126 through 145 )
40X-RAY DIFFRACTION40chain 'E' and (resid 146 through 195 )
41X-RAY DIFFRACTION41chain 'E' and (resid 196 through 220 )
42X-RAY DIFFRACTION42chain 'F' and (resid 1 through 16 )
43X-RAY DIFFRACTION43chain 'F' and (resid 17 through 30 )
44X-RAY DIFFRACTION44chain 'F' and (resid 31 through 62 )
45X-RAY DIFFRACTION45chain 'F' and (resid 63 through 83 )
46X-RAY DIFFRACTION46chain 'F' and (resid 84 through 104 )
47X-RAY DIFFRACTION47chain 'F' and (resid 105 through 125 )
48X-RAY DIFFRACTION48chain 'F' and (resid 126 through 145 )
49X-RAY DIFFRACTION49chain 'F' and (resid 146 through 160 )
50X-RAY DIFFRACTION50chain 'F' and (resid 161 through 176 )
51X-RAY DIFFRACTION51chain 'F' and (resid 177 through 195 )
52X-RAY DIFFRACTION52chain 'F' and (resid 196 through 221 )
53X-RAY DIFFRACTION53chain 'G' and (resid 1 through 16 )
54X-RAY DIFFRACTION54chain 'G' and (resid 17 through 30 )
55X-RAY DIFFRACTION55chain 'G' and (resid 31 through 43 )
56X-RAY DIFFRACTION56chain 'G' and (resid 44 through 83 )
57X-RAY DIFFRACTION57chain 'G' and (resid 84 through 104 )
58X-RAY DIFFRACTION58chain 'G' and (resid 105 through 125 )
59X-RAY DIFFRACTION59chain 'G' and (resid 126 through 145 )
60X-RAY DIFFRACTION60chain 'G' and (resid 146 through 160 )
61X-RAY DIFFRACTION61chain 'G' and (resid 161 through 176 )
62X-RAY DIFFRACTION62chain 'G' and (resid 177 through 205 )
63X-RAY DIFFRACTION63chain 'G' and (resid 206 through 219 )
64X-RAY DIFFRACTION64chain 'H' and (resid 1 through 16 )
65X-RAY DIFFRACTION65chain 'H' and (resid 17 through 30 )
66X-RAY DIFFRACTION66chain 'H' and (resid 31 through 62 )
67X-RAY DIFFRACTION67chain 'H' and (resid 63 through 83 )
68X-RAY DIFFRACTION68chain 'H' and (resid 84 through 104 )
69X-RAY DIFFRACTION69chain 'H' and (resid 105 through 125 )
70X-RAY DIFFRACTION70chain 'H' and (resid 126 through 145 )
71X-RAY DIFFRACTION71chain 'H' and (resid 146 through 160 )
72X-RAY DIFFRACTION72chain 'H' and (resid 161 through 176 )
73X-RAY DIFFRACTION73chain 'H' and (resid 177 through 195 )
74X-RAY DIFFRACTION74chain 'H' and (resid 196 through 210 )
75X-RAY DIFFRACTION75chain 'H' and (resid 211 through 221 )
76X-RAY DIFFRACTION76chain 'I' and (resid 1 through 16 )
77X-RAY DIFFRACTION77chain 'I' and (resid 17 through 30 )
78X-RAY DIFFRACTION78chain 'I' and (resid 31 through 62 )
79X-RAY DIFFRACTION79chain 'I' and (resid 63 through 83 )
80X-RAY DIFFRACTION80chain 'I' and (resid 84 through 104 )
81X-RAY DIFFRACTION81chain 'I' and (resid 105 through 125 )
82X-RAY DIFFRACTION82chain 'I' and (resid 126 through 145 )
83X-RAY DIFFRACTION83chain 'I' and (resid 146 through 174 )
84X-RAY DIFFRACTION84chain 'I' and (resid 175 through 192 )
85X-RAY DIFFRACTION85chain 'I' and (resid 193 through 205 )
86X-RAY DIFFRACTION86chain 'I' and (resid 206 through 221 )
87X-RAY DIFFRACTION87chain 'J' and (resid 1 through 16 )
88X-RAY DIFFRACTION88chain 'J' and (resid 17 through 30 )
89X-RAY DIFFRACTION89chain 'J' and (resid 31 through 62 )
90X-RAY DIFFRACTION90chain 'J' and (resid 63 through 83 )
91X-RAY DIFFRACTION91chain 'J' and (resid 84 through 110 )
92X-RAY DIFFRACTION92chain 'J' and (resid 111 through 125 )
93X-RAY DIFFRACTION93chain 'J' and (resid 126 through 144 )
94X-RAY DIFFRACTION94chain 'J' and (resid 145 through 160 )
95X-RAY DIFFRACTION95chain 'J' and (resid 161 through 175 )
96X-RAY DIFFRACTION96chain 'J' and (resid 176 through 192 )
97X-RAY DIFFRACTION97chain 'J' and (resid 193 through 203 )
98X-RAY DIFFRACTION98chain 'J' and (resid 204 through 219 )
99X-RAY DIFFRACTION99chain 'K' and (resid 1 through 16 )
100X-RAY DIFFRACTION100chain 'K' and (resid 17 through 30 )
101X-RAY DIFFRACTION101chain 'K' and (resid 31 through 62 )
102X-RAY DIFFRACTION102chain 'K' and (resid 63 through 83 )
103X-RAY DIFFRACTION103chain 'K' and (resid 84 through 125 )
104X-RAY DIFFRACTION104chain 'K' and (resid 126 through 145 )
105X-RAY DIFFRACTION105chain 'K' and (resid 146 through 160 )
106X-RAY DIFFRACTION106chain 'K' and (resid 161 through 175 )
107X-RAY DIFFRACTION107chain 'K' and (resid 176 through 195 )
108X-RAY DIFFRACTION108chain 'K' and (resid 196 through 210 )
109X-RAY DIFFRACTION109chain 'K' and (resid 211 through 219 )
110X-RAY DIFFRACTION110chain 'L' and (resid 1 through 110 )
111X-RAY DIFFRACTION111chain 'L' and (resid 111 through 145 )
112X-RAY DIFFRACTION112chain 'L' and (resid 146 through 219 )

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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