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- PDB-5gmz: Hepatitis B virus core protein Y132A mutant in complex with 4-met... -

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基本情報

登録情報
データベース: PDB / ID: 5gmz
タイトルHepatitis B virus core protein Y132A mutant in complex with 4-methyl heteroaryldihydropyrimidine
要素Core protein
キーワードVIRAL PROTEIN / HBV / capid assembly / HAP / core protein
機能・相同性
機能・相同性情報


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein binding
類似検索 - 分子機能
Hepatitis B viral capsid (hbcag) fold / Viral capsid, core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Chem-6XU / ISOPROPYL ALCOHOL / Capsid protein / Capsid protein
類似検索 - 構成要素
生物種Hepatitis B virus (B 型肝炎ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.7 Å
データ登録者Xu, Z.H. / Zhou, Z.
引用ジャーナル: J.Med.Chem. / 年: 2016
タイトル: Design and Synthesis of Orally Bioavailable 4-Methyl Heteroaryldihydropyrimidine Based Hepatitis B Virus (HBV) Capsid Inhibitors
著者: Qiu, Z. / Lin, X. / Zhou, M. / Liu, Y. / Zhu, W. / Chen, W. / Zhang, W. / Guo, L. / Liu, H. / Wu, G. / Huang, M. / Jiang, M. / Xu, Z. / Zhou, Z. / Qin, N. / Ren, S. / Qiu, H. / Zhong, S. / ...著者: Qiu, Z. / Lin, X. / Zhou, M. / Liu, Y. / Zhu, W. / Chen, W. / Zhang, W. / Guo, L. / Liu, H. / Wu, G. / Huang, M. / Jiang, M. / Xu, Z. / Zhou, Z. / Qin, N. / Ren, S. / Qiu, H. / Zhong, S. / Zhang, Y. / Zhang, Y. / Wu, X. / Shi, L. / Shen, F. / Mao, Y. / Zhou, X. / Yang, W. / Wu, J.Z. / Yang, G. / Mayweg, A.V. / Shen, H.C. / Tang, G.
履歴
登録2016年7月18日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02016年8月10日Provider: repository / タイプ: Initial release
改定 1.12016年9月7日Group: Database references
改定 1.22023年11月8日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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: Core protein
B: Core protein
C: Core protein
D: Core protein
E: Core protein
F: Core protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)109,26427
ポリマ－104,9216
非ポリマー4,34221
水13,403744
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18910 Å2
ΔGint-89 kcal/mol
Surface area41200 Å2
単位格子
Length a, b, c (Å)66.017, 67.215, 87.669
Angle α, β, γ (deg.)68.100, 68.430, 83.070
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 1 or (resid 2 and (name...
21(chain B and (resseq 1 or (resid 2 and (name...
31(chain C and (resseq 1 or (resid 2 and (name...
41(chain D and (resseq 1 or (resid 2 and (name...
51(chain E and (resseq 1 or (resid 2 and (name...
61(chain F and (resseq 1 or (resid 2 and (name...

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
11METMETMETMET(chain A and (resseq 1 or (resid 2 and (name...AA11
12ASPASPASPASP(chain A and (resseq 1 or (resid 2 and (name...AA22
13METMETLEULEU(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1431 - 143
14METMETLEULEU(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1431 - 143
15METMETLEULEU(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1431 - 143
16METMETLEULEU(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1431 - 143
17METMETLEULEU(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1431 - 143
18METMETLEULEU(chain A and (resseq 1 or (resid 2 and (name...AA1 - 1431 - 143
21METMETMETMET(chain B and (resseq 1 or (resid 2 and (name...BB11
22ASPASPASPASP(chain B and (resseq 1 or (resid 2 and (name...BB22
23METMETGLNGLN(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1551 - 155
24METMETGLNGLN(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1551 - 155
25METMETGLNGLN(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1551 - 155
26METMETGLNGLN(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1551 - 155
27METMETGLNGLN(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1551 - 155
28METMETGLNGLN(chain B and (resseq 1 or (resid 2 and (name...BB1 - 1551 - 155
31METMETMETMET(chain C and (resseq 1 or (resid 2 and (name...CC11
32ASPASPASPASP(chain C and (resseq 1 or (resid 2 and (name...CC22
33METMETLEULEU(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1431 - 143
34METMETLEULEU(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1431 - 143
35METMETLEULEU(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1431 - 143
36METMETLEULEU(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1431 - 143
37METMETLEULEU(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1431 - 143
38METMETLEULEU(chain C and (resseq 1 or (resid 2 and (name...CC1 - 1431 - 143
41METMETMETMET(chain D and (resseq 1 or (resid 2 and (name...DD11
42ASPASPASPASP(chain D and (resseq 1 or (resid 2 and (name...DD22
43METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
44METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
45METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
46METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
47METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
48METMETGLNGLN(chain D and (resseq 1 or (resid 2 and (name...DD1 - 1551 - 155
51METMETMETMET(chain E and (resseq 1 or (resid 2 and (name...EE11
52ASPASPASPASP(chain E and (resseq 1 or (resid 2 and (name...EE22
53METMETLEULEU(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1431 - 143
54METMETLEULEU(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1431 - 143
55METMETLEULEU(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1431 - 143
56METMETLEULEU(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1431 - 143
57METMETLEULEU(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1431 - 143
58METMETLEULEU(chain E and (resseq 1 or (resid 2 and (name...EE1 - 1431 - 143
61METMETMETMET(chain F and (resseq 1 or (resid 2 and (name...FF11
62ASPASPASPASP(chain F and (resseq 1 or (resid 2 and (name...FF22
63METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155
64METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155
65METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155
66METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155
67METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155
68METMETGLNGLN(chain F and (resseq 1 or (resid 2 and (name...FF1 - 1551 - 155

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要素

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タンパク質 , 1種, 6分子 ABCDEF

#1: タンパク質
Core protein


分子量: 17486.916 Da / 分子数: 6 / 断片: UNP residues 1-149 / 変異: Y132A / 由来タイプ: 組換発現
由来: (組換発現) Hepatitis B virus (B 型肝炎ウイルス)
遺伝子: C / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: L7R9I1, UniProt: P03147*PLUS

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非ポリマー , 5種, 765分子

#2: 化合物
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / 2-プロパノ-ル


分子量: 60.095 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C3H8O / コメント: alkaloid*YM
#3: 化合物
ChemComp-6XU / (2S)-4,4-difluoro-1-[[(4S)-4-(4-fluorophenyl)-5-methoxycarbonyl-4-methyl-2-(1,3-thiazol-2-yl)-1H-pyrimidin-6-yl]methyl]pyrrolidine-2-carboxylic acid


分子量: 494.487 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C22H21F3N4O4S
#4: 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
#5: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 744 / 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: 3.2 Å3/Da / 溶媒含有率: 61.55 %
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: 5.6
詳細: 100 mM citrate, 21%(v/v) isopropanol, 1% (w/v) PEG 10000

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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: SSRF / ビームライン: BL17U / 波長: 0.9793 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年3月7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: 0.9793 Å / 相対比: 1
反射解像度: 1.7→50 Å / Num. obs: 137833 / % possible obs: 96.4 % / 冗長度: 4.1 % / Biso Wilson estimate: 25.44 Å2 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.027 / Rrim(I) all: 0.055 / Χ2: 1.096 / Net I/av σ(I): 24.96 / Net I/σ(I): 10.9 / Num. measured all: 565211
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7341.00168360.6460.5761.1571.11595.2
1.73-1.7640.86967920.7320.4961.0011.14395.2
1.76-1.794.10.74268280.7980.4230.8551.13295.8
1.79-1.834.10.66468490.8560.3780.7651.17495.5
1.83-1.874.10.46268220.910.2630.5321.19595.7
1.87-1.914.10.40468540.9250.2290.4651.21695.9
1.91-1.964.10.33668670.9410.190.3871.23195.9
1.96-2.024.10.27668580.9520.1560.3171.25796.1
2.02-2.074.10.20768260.9740.1170.2381.21696.4
2.07-2.144.10.17469450.9810.0980.21.51796.6
2.14-2.224.10.1368880.9910.0730.151.22996.6
2.22-2.314.10.10169350.9940.0560.1151.19296.7
2.31-2.414.10.08369020.9950.0470.0961.15497.1
2.41-2.544.10.07169610.9960.040.0811.1597
2.54-2.74.10.05969240.9970.0330.0671.1397.3
2.7-2.914.10.04669310.9980.0260.0531.06996.9
2.91-3.24.10.03669300.9990.020.0410.95297
3.2-3.664.10.02668940.9990.0140.030.7496.2
3.66-4.614.20.02170640.9990.0110.0240.57799
4.61-504.20.02269270.9990.0120.0250.57997

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
SCALEPACKデータスケーリング
PDB_EXTRACT3.2データ抽出
HKL-2000データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4BMG

4bmg


解像度: 1.7→33.308 Å / SU ML: 0.19 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 23.87 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1963 3334 2.42 %
Rwork0.1736 134437 -
obs0.1742 137771 96.26 %
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: 175.65 Å2 / Biso mean: 41.0333 Å2 / Biso min: 17.92 Å2
精密化ステップサイクル: final / 解像度: 1.7→33.308 Å
タンパク質核酸リガンド溶媒全体
原子数6967 0 295 744 8006
Biso mean--36.07 48.44 -
残基数----877
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0117635
X-RAY DIFFRACTIONf_angle_d0.96410517
X-RAY DIFFRACTIONf_chiral_restr0.0491168
X-RAY DIFFRACTIONf_plane_restr0.0071327
X-RAY DIFFRACTIONf_dihedral_angle_d19.1664394
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3248X-RAY DIFFRACTION9.063TORSIONAL
12B3248X-RAY DIFFRACTION9.063TORSIONAL
13C3248X-RAY DIFFRACTION9.063TORSIONAL
14D3248X-RAY DIFFRACTION9.063TORSIONAL
15E3248X-RAY DIFFRACTION9.063TORSIONAL
16F3248X-RAY DIFFRACTION9.063TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6997-1.72390.31661240.31355351547592
1.7239-1.74970.36511440.29615473561795
1.7497-1.7770.26711410.2845570571196
1.777-1.80610.33411210.27675570569195
1.8061-1.83730.28961470.25815549569695
1.8373-1.87070.30591370.23425576571396
1.8707-1.90670.27981360.21465553568996
1.9067-1.94560.21881410.21685566570796
1.9456-1.98790.20581430.21185602574596
1.9879-2.03410.25941380.19715625576396
2.0341-2.0850.241300.19015592572296
2.085-2.14130.2711310.19785622575397
2.1413-2.20430.23261540.17855654580897
2.2043-2.27550.17251480.17445607575597
2.2755-2.35680.18721320.16125612574497
2.3568-2.45110.17791480.16855677582597
2.4511-2.56260.19131370.17755599573697
2.5626-2.69770.20581420.17245691583397
2.6977-2.86660.21141410.17735648578997
2.8666-3.08780.20541390.17815596573597
3.0878-3.39830.18321420.16995651579396
3.3983-3.88930.17591370.15085645578298
3.8893-4.89770.13841390.13245794593399
4.8977-33.31450.17531420.165614575697
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)
10.00250.00730.00380.0130.00280.0369-0.2276-0.2867-0.1563-0.05310.2702-0.05160.29260.39340.00010.27960.0038-0.01810.3917-0.06880.2616-29.854-4.804119.4065
20.017-0.05780.00270.0441-0.02570.0632-0.23070.1303-0.26110.18470.18680.22330.28850.239100.35970.05110.02110.3531-0.0060.2677-41.3983-3.314229.5126
30.1403-0.01010.01980.06390.12510.12180.23960.17060.2179-0.1763-0.06880.1788-0.3416-0.2623-0.00020.3086-0.0510.04520.235-0.0170.2748-45.708410.623815.7358
40.896-0.2907-0.43870.09520.14460.21380.35050.2260.4719-0.15720.06870.1247-0.3213-0.11680.00370.5847-0.25040.14640.1211-0.10950.4444-32.571312.80148.2869
50.0888-0.0811-0.0750.2507-0.22090.30930.0094-0.1453-0.1322-0.06440.0642-0.0337-0.0786-0.0470.00660.2312-0.11190.03310.2359-0.03350.3208-45.7999-1.79259.9377
60.03740.00010.04720.0902-0.0710.02230.2378-0.29870.17110.2131-0.10320.34130.0893-0.0506-0.00010.3852-0.16130.06780.4226-0.06140.5591-58.3159-12.603215.8864
70.0888-0.0319-0.0110.0275-0.04760.0872-0.060.0258-0.0581-0.03470.0934-0.0040.08760.13180.00010.2808-0.04080.00580.257-0.05020.2561-40.37132.358422.2572
80.5172-0.2783-0.07760.3337-0.2130.3052-0.3749-0.46720.03920.42890.4213-0.1068-0.1390.16930.03390.30250.0149-0.02920.3036-0.04990.2522-36.03923.501534.5125
90.0187-0.00270.0450.0063-0.07990.0809-0.1872-0.17150.0370.10060.24420.2061-0.23-0.13-0.00020.39910.12110.01320.36770.00130.243-42.90454.330542.0111
100.0768-0.0451-0.07290.01820.03120.17040.12630.20560.269-0.21730.05690.0004-0.7206-0.26440.00240.3307-0.04170.06170.2888-0.00370.3209-38.16987.27082.578
110.0208-0.027-0.01060.01970.03220.05320.32240.0497-0.0548-0.1964-0.3650.118-0.1273-0.0362-0.00020.3090.02310.01030.3165-0.01310.2651-37.5424-3.3534-8.5315
120.0274-0.0185-0.02680.04240.0510.06530.0008-0.1928-0.11990.0770.1547-0.0370.42810.33880.00020.1919-0.01080.00130.325-0.01090.2498-26.6133-11.59865.2462
130.4171-0.1509-0.3020.8331-0.04340.2288-0.0973-0.3388-0.01210.27630.2425-0.33270.06870.02550.09420.0023-0.2954-0.08750.6281-0.23690.3831-23.1763-1.370315.167
140.2135-0.0639-0.2080.0145-0.07770.5003-0.11230.1738-0.0899-0.04960.15690.05110.0839-0.06740.00090.235-0.11680.0110.2824-0.03090.3366-44.6836-12.99716.6944
150.0198-0.05280.01880.14090.05730.14950.05790.14030.0390.052-0.0133-0.01580.0489-0.0573-00.2243-0.02520.01640.2964-0.02140.262-32.661-4.1015-0.7815
160.2346-0.28640.30930.2163-0.23820.3510.38420.20920.0512-0.3402-0.355-0.22540.16370.1523-0.01990.2850.03980.02710.29270.02280.2467-30.2194-0.9564-15.9019
170.13980.0069-0.00060.6095-0.17440.4457-0.02990.0572-0.37410.1331-0.42420.13970.1349-0.2182-0.24310.4549-0.14640.3280.35910.02540.6474-22.214.785-1.303
18-0.0024-0.0084-0.0060.012-0.00510.013-0.0974-0.1980.25640.0450.19520.3118-0.1403-0.1185-0.00050.2844-0.0499-0.00050.32010.02510.2754-14.5514-26.596315.0616
190.0065-0.01060.00840.011-0.0130.0039-0.1366-0.18970.10320.31380.1257-0.0818-0.40360.0391-0.00040.2466-0.05240.00720.23160.0140.3368-10.6063-21.333810.6092
200.009-0.0142-0.00320.0180.01020.0150.1267-0.11170.0165-0.0979-0.1768-0.2179-0.184-0.120500.2344-0.0239-0.02530.30630.04310.2848-20.8794-21.27135.0138
210.01470.0051-0.01740.0128-0.02730.03230.18170.0442-0.0126-0.0759-0.1161-0.03350.0582-0.212600.2477-0.0396-0.03050.2217-0.01970.2566-20.314-26.6755-4.3546
220.06250.0331-0.01650.0516-0.00690.0350.29180.293-0.1623-0.3903-0.2692-0.07310.51950.4891-00.35780.06560.02850.37180.04430.2835-4.8354-35.1292-4.6844
230.2166-0.1666-0.34270.14640.23940.484-0.0838-0.0468-0.0081-0.1863-0.1179-0.08240.24690.2214-0.00490.228-0.0798-0.01780.25410.02790.2633-8.0246-39.41215.4041
240.04670.0267-0.05450.058-0.11170.276-0.3350.29070.1249-0.2194-0.09210.07240.4517-0.5913-0.5018-0.0261-0.9359-0.05860.48150.08020.5604-28.2143-46.05790.9283
250.1028-0.06470.12970.0141-0.06270.1060.10720.0429-0.0856-0.0552-0.0785-0.02360.11450.0312-0.00010.2345-0.0166-0.00220.2760.03910.2589-12.179-28.19680.6212
260.6397-0.2695-0.30650.14340.14720.46760.1350.28770.1803-0.1949-0.2007-0.1248-0.397-0.12530.00250.2276-0.01710.01490.19540.03840.2759-16.5572-16.2564-3.3122
270.03810.01190.00820.089-0.07640.02140.24730.2658-0.0172-0.283-0.3182-0.1175-0.05530.07960.00020.33010.08680.01620.36080.01090.2619-20.1633-14.9112-12.6062
280.0233-0.06050.02160.0523-0.01720.0130.18430.3671-0.0256-0.3238-0.3426-0.1830.22560.483-0.00030.24930.0066-0.01250.32080.03290.28972.2818-40.148.7812
290.0567-0.0860.03150.063-0.02540.0248-0.21940.09360.0140.10320.1018-0.0040.36590.1283-0.00020.2683-0.02770.00920.28660.03930.2785-0.5774-49.041921.2766
300.116-0.03970.01480.0108-0.02930.0636-0.1531-0.249-0.04910.49540.16220.1422-0.3602-0.272100.3221-0.0229-0.03590.25060.00520.2466-9.9717-32.841326.2694
310.2638-0.3181-0.08770.5107-0.22050.3885-0.18440.0530.04140.34550.25540.1358-0.1053-0.15320.13920.0547-0.3675-0.07510.10210.04710.3155-13.2429-34.696714.7533
320.0466-0.01640.02230.0684-0.01730.0190.1386-0.0676-0.1968-0.3561-0.1318-0.26540.526-0.18490.00530.5647-0.263-0.03130.54330.04240.7401-22.5235-54.261115.1957
33-0.00520.0017-0.02650.0989-0.12110.0984-0.17670.07720.031-0.0410.2143-0.0182-0.07960.0215-0.00010.234-0.0477-0.03460.21980.01180.2417-3.1522-40.446920.6922
340.1712-0.24220.00990.1817-0.0529-0.0033-0.2378-0.11240.04090.26940.1828-0.07160.07010.16320.00160.26490.0326-0.01240.27960.00010.24377.4094-49.913728.296
350.5831-0.3706-0.85731.32550.11681.2526-0.24290.03990.38410.02640.1778-0.07580.0280.76050.07280.2545-0.195-0.13430.37720.04080.457.6581-31.570223.1009
360.0011-0.0027-0.01340.03270.01650.02740.17890.38810.2253-0.2977-0.2139-0.0465-0.0049-0.15040.00030.39550.15790.05820.37270.05340.3468-18.9742-19.804138.7652
370.0439-0.0121-0.03560.00610.00740.02270.1866-0.08650.172-0.2094-0.00380.13030.0196-0.37050.00130.36790.12280.02190.4090.02640.3329-15.607-30.698835.56
380.0176-0.0024-0.00870.0105-0.00110.01180.03810.0983-0.0071-0.13360.18610.1490.35150.0001-0.00010.42020.09230.02730.32470.00120.2641-15.4567-37.949543.484
390.0496-0.00610.04510.0370.00490.0239-0.4393-0.33760.02780.56960.26490.05290.0804-0.1281-0.00010.41740.1569-0.04610.3819-0.02990.2994-17.084-29.251758.7391
400.4346-0.5238-0.02830.4941-0.04940.4029-0.1653-0.16690.0620.39860.3636-0.03130.0213-0.1650.00010.36610.0873-0.0270.33220.01610.3886-26.5007-24.623853.7118
410.00050.0023-0.0032-0.001-0.00160.01670.1198-0.0549-0.22960.11120.08060.31760.26810.09190.00030.5812-0.0169-0.03610.49140.04180.7375-36.4785-41.859945.7349
420.0224-0.0286-0.04730.12530.03310.04570.01660.08610.1991-0.05310.03370.0226-0.0265-0.09250.00010.32880.0985-0.02190.3088-0.00430.3115-16.2617-29.143747.3851
430.0272-0.0722-0.08020.03870.08440.01440.046-0.03520.076-0.0978-0.0577-0.17640.21920.06880.00010.2890.06940.02260.27730.01670.2502-5.7909-35.623938.6951
440.0331-0.0009-0.00540.01760.03860.03370.0039-0.08270.10730.1356-0.0759-0.24990.48190.1919-0.00020.37120.11510.00110.32830.0060.2803-1.119-39.725844.0336
450.1041-0.1227-0.17320.0849-0.04720.2039-0.1961-0.206-0.02620.19470.2034-0.1020.1794-0.11230.00080.4170.1598-0.01040.3095-0.02640.2789-33.0143-12.182558.0704
460.03940.03440.05820.0920.18580.590.20810.51830.1833-0.429-0.3041-0.17620.3715-0.2377-0.01330.42960.18060.07060.31380.05540.3216-31.4497-9.974239.1439
470.3767-0.4740.22770.4426-0.06540.12890.29720.15630.1171-0.2457-0.0675-0.12730.0133-0.10880.01150.35170.0799-0.02740.34690.03230.3859-29.0207-21.058442.8868
480.00320.00270.0032-0.00570.00870.0007-0.11310.0778-0.193-0.1811-0.10990.1350.2333-0.1449-0.00040.6629-0.0297-0.05541.17610.13391.5164-47.2049-29.573244.5465
490.1275-0.0870.03990.0326-0.02110.03930.15030.018-0.05860.18760.0284-0.09210.0885-0.02200.34880.10860.01460.30070.0230.3278-32.8536-10.3950.397
500.08310.0032-0.15350.05490.06210.07380.11910.21870.0757-0.0414-0.0974-0.1428-0.2027-0.20540.00010.34460.0920.00310.2867-0.00710.2398-40.17351.32157.9725
510.00020.0095-0.0049-0.0037-0.0042-0.0064-0.0092-0.18960.0079-0.0298-0.03790.0461-0.14140.1027-0.00010.7633-0.0233-0.06940.73380.09410.5946-22.248825.196454.7478
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 26 )A13 - 26
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 43 )A27 - 43
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 49 )A44 - 49
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 75 )A50 - 75
6X-RAY DIFFRACTION6chain 'A' and (resid 76 through 92 )A76 - 92
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 110 )A93 - 110
8X-RAY DIFFRACTION8chain 'A' and (resid 111 through 126 )A111 - 126
9X-RAY DIFFRACTION9chain 'A' and (resid 127 through 143 )A127 - 143
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 12 )B1 - 12
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 26 )B13 - 26
12X-RAY DIFFRACTION12chain 'B' and (resid 27 through 42 )B27 - 42
13X-RAY DIFFRACTION13chain 'B' and (resid 43 through 49 )B43 - 49
14X-RAY DIFFRACTION14chain 'B' and (resid 50 through 92 )B50 - 92
15X-RAY DIFFRACTION15chain 'B' and (resid 93 through 110 )B93 - 110
16X-RAY DIFFRACTION16chain 'B' and (resid 111 through 137 )B111 - 137
17X-RAY DIFFRACTION17chain 'B' and (resid 138 through 155 )B138 - 155
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 6 )C1 - 6
19X-RAY DIFFRACTION19chain 'C' and (resid 7 through 12 )C7 - 12
20X-RAY DIFFRACTION20chain 'C' and (resid 13 through 18 )C13 - 18
21X-RAY DIFFRACTION21chain 'C' and (resid 19 through 26 )C19 - 26
22X-RAY DIFFRACTION22chain 'C' and (resid 27 through 42 )C27 - 42
23X-RAY DIFFRACTION23chain 'C' and (resid 43 through 75 )C43 - 75
24X-RAY DIFFRACTION24chain 'C' and (resid 76 through 92 )C76 - 92
25X-RAY DIFFRACTION25chain 'C' and (resid 93 through 110 )C93 - 110
26X-RAY DIFFRACTION26chain 'C' and (resid 111 through 127 )C111 - 127
27X-RAY DIFFRACTION27chain 'C' and (resid 128 through 143 )C128 - 143
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 12 )D1 - 12
29X-RAY DIFFRACTION29chain 'D' and (resid 13 through 26 )D13 - 26
30X-RAY DIFFRACTION30chain 'D' and (resid 27 through 42 )D27 - 42
31X-RAY DIFFRACTION31chain 'D' and (resid 43 through 75 )D43 - 75
32X-RAY DIFFRACTION32chain 'D' and (resid 76 through 92 )D76 - 92
33X-RAY DIFFRACTION33chain 'D' and (resid 93 through 110 )D93 - 110
34X-RAY DIFFRACTION34chain 'D' and (resid 111 through 137 )D111 - 137
35X-RAY DIFFRACTION35chain 'D' and (resid 138 through 155 )D138 - 155
36X-RAY DIFFRACTION36chain 'E' and (resid 1 through 12 )E1 - 12
37X-RAY DIFFRACTION37chain 'E' and (resid 13 through 18 )E13 - 18
38X-RAY DIFFRACTION38chain 'E' and (resid 19 through 26 )E19 - 26
39X-RAY DIFFRACTION39chain 'E' and (resid 27 through 42 )E27 - 42
40X-RAY DIFFRACTION40chain 'E' and (resid 43 through 75 )E43 - 75
41X-RAY DIFFRACTION41chain 'E' and (resid 76 through 92 )E76 - 92
42X-RAY DIFFRACTION42chain 'E' and (resid 93 through 110 )E93 - 110
43X-RAY DIFFRACTION43chain 'E' and (resid 111 through 132 )E111 - 132
44X-RAY DIFFRACTION44chain 'E' and (resid 133 through 143 )E133 - 143
45X-RAY DIFFRACTION45chain 'F' and (resid 1 through 26 )F1 - 26
46X-RAY DIFFRACTION46chain 'F' and (resid 27 through 42 )F27 - 42
47X-RAY DIFFRACTION47chain 'F' and (resid 43 through 76 )F43 - 76
48X-RAY DIFFRACTION48chain 'F' and (resid 77 through 92 )F77 - 92
49X-RAY DIFFRACTION49chain 'F' and (resid 93 through 110 )F93 - 110
50X-RAY DIFFRACTION50chain 'F' and (resid 111 through 142 )F111 - 142
51X-RAY DIFFRACTION51chain 'F' and (resid 143 through 155 )F143 - 155

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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://pdbjlvh1.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