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- PDB-5yod: Crystal structure of zika virus NS3 protease in complex with a sm... -

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基本情報

登録情報
データベース: PDB / ID: 5yod
タイトルCrystal structure of zika virus NS3 protease in complex with a small molecule inhibitor
要素
  • NS2B cofactor
  • NS3 protease
キーワードVIRAL PROTEIN/INHIBITOR / Non-structural protein 3 / serine protease / zika viral protease / VIRAL PROTEIN-INHIBITOR complex
機能・相同性
機能・相同性情報


symbiont-mediated suppression of host interferon-mediated signaling pathway / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway ...symbiont-mediated suppression of host interferon-mediated signaling pathway / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / protein-macromolecule adaptor activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
類似検索 - 分子機能
Thrombin, subunit H - #120 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B ...Thrombin, subunit H - #120 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
類似検索 - ドメイン・相同性
BENZOIC ACID / Genome polyprotein
類似検索 - 構成要素
生物種Zika virus (ジカ熱ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.9 Å
データ登録者Phoo, W.W. / Zhang, Z.Z.
資金援助 シンガポール, 2件
組織認可番号国
NTUSTART UP GRANT シンガポール
NMRCCBRG14May05 シンガポール
引用ジャーナル: Structure / 年: 2018
タイトル: Structural Insights into the Inhibition of Zika Virus NS2B-NS3 Protease by a Small-Molecule Inhibitor
著者: Li, Y. / Zhang, Z. / Phoo, W.W. / Loh, Y.R. / Li, R. / Yang, H.Y. / Jansson, A.E. / Hill, J. / Keller, T.H. / Nacro, K. / Luo, D. / Kang, C.
履歴
登録2017年10月27日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02018年3月21日Provider: repository / タイプ: Initial release
改定 1.12018年4月4日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22018年4月25日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年11月22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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: NS2B cofactor
B: NS3 protease
C: NS2B cofactor
D: NS3 protease
E: NS2B cofactor
F: NS3 protease
G: NS2B cofactor
H: NS3 protease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,03612
ポリマ－99,5488
非ポリマー4884
水5,224290
1
A: NS2B cofactor
B: NS3 protease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,0093
ポリマ－24,8872
非ポリマー1221
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-25 kcal/mol
Surface area9130 Å2
手法PISA
2
C: NS2B cofactor
D: NS3 protease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,0093
ポリマ－24,8872
非ポリマー1221
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-23 kcal/mol
Surface area9120 Å2
手法PISA
3
E: NS2B cofactor
F: NS3 protease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,0093
ポリマ－24,8872
非ポリマー1221
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-25 kcal/mol
Surface area8790 Å2
手法PISA
4
G: NS2B cofactor
H: NS3 protease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,0093
ポリマ－24,8872
非ポリマー1221
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-27 kcal/mol
Surface area8860 Å2
手法PISA
単位格子
Length a, b, c (Å)59.366, 59.628, 215.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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要素

#1: タンパク質
NS2B cofactor


分子量: 5865.384 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Zika virus (ジカ熱ウイルス) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q32ZE1*PLUS
#2: タンパク質
NS3 protease


分子量: 19021.527 Da / 分子数: 4 / Mutation: C144S / 由来タイプ: 組換発現 / 由来: (組換発現) Zika virus (ジカ熱ウイルス) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q32ZE1*PLUS
#3: 化合物
ChemComp-BEZ / BENZOIC ACID / 安息香酸


分子量: 122.121 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C7H6O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 290 / 由来タイプ: 天然 / 式: H2O
非ポリマーの詳細Authors state that the ligand BEZ is a derivative from the original ligand, 5-amino-1-((4- ...Authors state that the ligand BEZ is a derivative from the original ligand, 5-amino-1-((4-methoxyphenyl)sulfonyl)-1H-pyrazol-3-yl benzoate (compound 1).

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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: 2.04 Å3/Da / 溶媒含有率: 35.73 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.6
詳細: 0.2M Ammonium sulfate, 0.1M Sodium acetate trihydrate pH 4.6, 25% PEG4000
PH範囲: 5

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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: Australian Synchrotron / ビームライン: MX1 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2017年6月23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: 0.9537 Å / 相対比: 1
反射解像度: 1.9→45.74 Å / Num. obs: 61049 / % possible obs: 99.6 % / 冗長度: 6 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.058 / Net I/σ(I): 9.9
反射 シェル解像度: 1.9→1.94 Å / 冗長度: 5.7 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2 / Num. unique obs: 3898 / CC1/2: 0.533 / Rpim(I) all: 0.522 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.12_2829: ???)精密化
iMOSFLMデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5H6V

5h6v


解像度: 1.9→42.07 Å / 交差検証法: FREE R-VALUE / σ(F): 16.61 / 位相誤差: 37.15 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射Selection details
Rfree0.2683 3113 5.1 %Random selection
Rwork0.2417 ---
obs0.2483 60987 99.46 %-
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: 1.9→42.07 Å
タンパク質核酸リガンド溶媒全体
原子数5641 0 32 290 5963
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.015784
X-RAY DIFFRACTIONf_angle_d1.057852
X-RAY DIFFRACTIONf_dihedral_angle_d8.0323354
X-RAY DIFFRACTIONf_chiral_restr0.05869
X-RAY DIFFRACTIONf_plane_restr0.0041016
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.93280.36511620.36212868X-RAY DIFFRACTION95
1.9328-1.9680.361160.34922889X-RAY DIFFRACTION96
1.968-2.00580.37031460.32622854X-RAY DIFFRACTION95
2.0058-2.04680.38411570.32512907X-RAY DIFFRACTION95
2.0468-2.09130.36041700.32382806X-RAY DIFFRACTION94
2.0913-2.13990.3451760.30362869X-RAY DIFFRACTION94
2.1399-2.19340.26521530.2882864X-RAY DIFFRACTION95
2.1934-2.25270.34321740.28442852X-RAY DIFFRACTION94
2.2527-2.3190.32181440.28512884X-RAY DIFFRACTION95
2.319-2.39380.2761510.29882892X-RAY DIFFRACTION95
2.3938-2.47930.31851310.29182921X-RAY DIFFRACTION95
2.4793-2.57860.31881670.27792855X-RAY DIFFRACTION94
2.5786-2.69590.33671580.26752897X-RAY DIFFRACTION94
2.6959-2.8380.3071450.24622899X-RAY DIFFRACTION95
2.838-3.01570.23861580.23492879X-RAY DIFFRACTION94
3.0157-3.24840.27931520.21882919X-RAY DIFFRACTION95
3.2484-3.5750.23631390.21472901X-RAY DIFFRACTION94
3.575-4.09160.2281780.19452904X-RAY DIFFRACTION93
4.0916-5.15230.21031540.17742954X-RAY DIFFRACTION93
5.1523-34.91270.24621520.27313076X-RAY DIFFRACTION92
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)
13.51831.08860.14112.880.65310.92420.009-0.09670.06710.12110.0106-0.2024-0.03720.1390.01720.2818-0.010.03910.151-0.03210.21423.628644.539514.0861
23.73772.34560.97253.98362.03562.3771-0.03050.0412-0.0448-0.0237-0.05740.04020.0204-0.09980.03270.3360.08470.04270.20150.02310.106513.273840.17133.4647
31.0732-0.9916-0.13241.0055-0.15330.95060.07370.16970.1782-0.18410.0085-0.1664-0.02870.0914-0.05290.52320.0156-0.04950.3857-0.03960.17414.129827.1432-5.6971
42.6976-2.60634.23483.8477-2.28039.1145-0.03020.1318-0.0884-0.1936-0.0597-0.03510.0959-0.07790.08930.29040.00890.04030.2569-0.12820.264220.314111.61363.6547
51.4898-0.8454-0.7561.0924-0.10490.8488-0.0265-0.0005-0.05420.12150.0269-0.09430.13960.1446-0.05030.32340.0311-0.11130.29060.08420.206622.827413.48118.1458
61.4613-0.06950.10872.49340.56091.3498-0.01170.0289-0.0310.0592-0.01140.01750.04280.00620.01240.33140.0151-0.20460.2954-0.00340.505825.371116.637718.6962
70.161-0.0001-0.02480.01730.01550.52510.0821-0.11890.06230.09090.0196-0.0899-0.0277-0.02430.1450.3301-0.038-0.02550.1438-0.0178-0.115418.550438.118416.3313
80.51710.07970.03240.74630.09960.52890.09370.0295-0.0965-0.0244-0.0159-0.0988-0.0729-0.1098-0.03670.2432-0.01260.00380.1979-0.0060.135716.544624.34097.174
92.8751-0.6676-1.56194.143-0.45571.0544-0.01630.02950.0703-0.1276-0.01060.2452-0.0327-0.24860.01310.32750.05760.06050.18410.04070.27875.640374.4125-13.4091
105.8595-4.1541.90615.7763-2.91672.6448-0.0429-0.0250.03060.03-0.0521-0.1172-0.04820.12220.04850.2997-0.12560.05040.2098-0.0550.139816.803469.9472-3.4935
110.11820.16330.17860.27990.06130.88480.0715-0.17050.11080.2135-0.01770.1643-0.0459-0.0391-0.040.5268-0.0692-0.07120.31850.02670.213516.740356.98495.6122
123.96910.5933.14114.29010.18362.5145-0.0216-0.0558-0.0620.1649-0.0370.05450.19430.06850.07090.3148-0.01840.00580.20640.10360.27329.81541.3732-3.1275
130.36940.13410.12020.15110.160.17110.078-0.0776-0.05630.0296-0.01630.03510.2012-0.0611-0.06240.3773-0.1038-0.07120.2915-0.06230.15976.040743.3495-17.3835
141.6226-0.45020.80271.37880.20830.736-0.03530.0241-0.0812-0.08860.05620.12850.1664-0.1412-0.0240.2986-0.0644-0.06160.27790.01720.21953.382446.5702-18.362
152.6945-0.59250.09111.1227-0.21241.1665-0.01440.09790.2365-0.00080.01380.0001-0.13340.1645-0.00250.31770.001-0.01030.1495-0.02910.15312.476271.8735-9.3507
161.02080.17270.18940.9954-0.11080.92170.04840.05830.043-0.03260.04040.2141-0.0884-0.0919-0.02630.29850.0313-0.01180.16660.00820.08119.124966.8489-13.7211
172.32471.64750.36012.48550.29331.94080.0133-0.03570.2506-0.0845-0.02550.204-0.23120.01150.03810.32490.0365-0.06260.33310.05620.22049.008174.8349-19.5193
180.12810.03520.01840.0279-0.08320.43360.03240.1096-0.0706-0.06360.0513-0.0842-0.03730.0953-0.02620.35270.0194-0.04730.2436-0.02390.050617.132957.928-16.4835
191.9111-1.3198-0.16092.53140.3430.85010.0045-0.14930.11960.16760.05480.1079-0.08430.008-0.02280.3399-0.06520.00450.1916-0.01690.1499.726262.8873-0.0395
200.72530.20550.41241.2809-0.11331.22450.0374-0.0006-0.03030.0887-0.0130.00330.009-0.0136-0.00780.28570.06390.01590.2220.0260.084913.197749.1127-3.4005
210.9609-0.6126-0.1871.35990.00080.52210.13120.0448-0.03720.051-0.02270.12880.08770.0406-0.01370.23830.0375-0.00930.17990.0050.15888.667751.6167-8.5644
225.142-0.12012.23742.1109-0.65942.72150.0134-0.016-0.04890.0416-0.0032-0.28730.13140.29420.00490.3481-0.0155-0.0130.18-0.02210.162820.93757.6914-4.4555
230.08510.05980.0650.33460.1050.89780.0026-0.0427-0.00070.0157-0.0040.0420.072-0.07870.01810.32570.06460.03320.1796-0.00010.04789.743253.9341-9.7104
240.06780.2867-0.07351.3187-0.38620.1310.0148-0.088-0.06740.138-0.02360.23790.1058-0.1536-0.00750.43140.11180.0460.337-0.03030.28151.08246.5271-5.2838
252.11350.4369-0.73331.6072-0.6042.7240.05670.16180.143-0.1565-0.0046-0.1298-0.14430.1152-0.03980.35860.09950.04710.19070.00590.156418.142255.0162-15.1137
262.0871-0.6116-0.7892.7010.83531.4007-0.0203-0.06250.16560.0289-0.04560.0968-0.1767-0.11970.06250.37950.07690.04440.34570.01740.2719-1.446568.1555-39.39
273.3729-3.2434-2.55674.89862.09942.0104-0.0412-0.0092-0.0439-0.0229-0.02330.0450.0474-0.07090.0490.35080.0459-0.02520.2380.09740.20282.511557.4712-49.8647
281.230.7316-0.57670.8619-0.61480.47250.00060.08940.0191-0.12090.00640.0179-0.0079-0.0111-0.00680.49680.06950.00820.61720.04940.308414.79257.7155-60.0991
293.1461-0.28980.69422.11271.52662.4125-0.01370.0652-0.03230.06840.0301-0.13940.02190.2514-0.00890.3854-0.07470.12930.40390.02410.324330.775665.2637-51.0809
300.01080.00230.00290.00620.00540.0047-0.0117-0.1084-0.0057-0.0174-0.0107-0.08180.00520.2120.0120.4499-0.0510.00910.4654-0.06780.234929.548968.4183-36.9019
311.33320.07440.19760.60750.20770.09350.0265-0.12370.01410.09190.03170.0022-0.01610.0675-0.00990.46430.05110.07630.30.02160.274926.144970.843-35.5871
320.32890.2386-0.05340.7412-0.19511.14370.04380.09620.083-0.00240.07530.1477-0.1774-0.26650.00550.39510.062-0.00750.3280.01010.08845.582663.4539-37.4174
330.55660.1646-0.21970.6788-0.06110.5156-0.11460.0552-0.0407-0.11510.0598-0.0893-0.042-0.08170.03270.38650.0071-0.00890.23030.01820.138518.325961.4662-47.0549
344.9752-0.38610.71785.0007-0.79670.3284-0.007-0.05360.04650.0371-0.0390.0617-0.0296-0.00260.040.25760.06040.00610.19970.06780.509732.270438.7404-41.5564
355.8725-3.1052-2.11176.06630.88821.533-0.0723-0.0647-0.10290.0550.0539-0.17530.15310.14120.01760.34840.0031-0.02210.2913-0.01680.18437.825528.0597-51.3734
361.59161.4714-0.15041.4554-0.34160.4439-0.07280.25380.0287-0.26340.07010.0671-0.0085-0.0058-0.01910.4819-0.03840.02550.4885-0.02370.269350.915828.0101-59.4715
370.84310.53541.30870.33990.83644.3175-0.0308-0.03260.03540.0226-0.0249-0.048-0.1023-0.01460.05870.34530.00530.06870.4162-0.00920.352266.156935.0161-48.4064
381.71041.03450.83162.633-0.54291.56230.0292-0.05740.06160.0334-0.00740.0012-0.08380.0272-0.02360.53880.02130.01290.37840.01520.319862.894638.3131-34.7318
394.3208-0.3777-5.49165.3837-1.02797.40410.0039-0.2162-0.00190.3302-0.0265-0.0931-0.06630.28510.00450.3884-0.05140.04750.34-0.00760.298456.505540.2134-32.087
400.7842-0.1554-1.97682.8836-1.10235.7657-0.0487-0.1107-0.0930.1707-0.0176-0.43820.08380.4260.06730.377-0.15940.00580.31720.02410.450765.876842.4114-37.1245
411.0081-0.631-0.39871.89780.7051.73720.0278-0.0554-0.01810.0356-0.04670.33140.0348-0.19740.02640.32030.0883-0.05060.5162-0.00380.292235.085634.4365-45.0439
420.61070.28770.11220.61510.16970.65730.0535-0.01310.01490.055-0.0109-0.023-0.0156-0.0005-0.020.4333-0.0666-0.01660.34490.06070.143541.41832.7356-39.7901
430.0921-0.254-0.42233.9751-0.65262.95180.0386-0.0226-0.046-0.23550.04690.45750.1574-0.5343-0.02420.4555-0.0257-0.07840.4226-0.02310.342731.328335.1619-35.5149
440.25890.04340.23790.0460.11460.3621-0.00260.07840.0111-0.02180.0178-0.0084-0.03270.01290.00090.4933-0.0108-0.06050.3037-0.00640.079745.347431.6905-31.6429
450.35280.04-0.26820.2868-0.11320.22220.03860.1758-0.0577-0.0867-0.0285-0.09870.11240.01780.01390.41050.0077-0.00640.26760.02980.23651.867129.4868-48.128
460.57040.2496-0.14590.6930.29580.2583-0.0825-0.1797-0.03390.13660.0551-0.10470.04560.01970.00570.2814-0.0505-0.00050.27750.01260.223555.601536.1155-44.3035
471.0726-0.15880.39971.19170.40291.2705-0.0420.0330.0711-0.12910.0813-0.11530.0936-0.0135-0.01670.39220.05190.02670.2230.00430.169853.793832.7173-45.0168
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 79 )
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 87 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 79 )
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 170 )
9X-RAY DIFFRACTION9chain 'C' and (resid 50 through 54 )
10X-RAY DIFFRACTION10chain 'C' and (resid 55 through 59 )
11X-RAY DIFFRACTION11chain 'C' and (resid 60 through 69 )
12X-RAY DIFFRACTION12chain 'C' and (resid 70 through 74 )
13X-RAY DIFFRACTION13chain 'C' and (resid 75 through 79 )
14X-RAY DIFFRACTION14chain 'C' and (resid 80 through 87 )
15X-RAY DIFFRACTION15chain 'D' and (resid 17 through 27 )
16X-RAY DIFFRACTION16chain 'D' and (resid 28 through 53 )
17X-RAY DIFFRACTION17chain 'D' and (resid 54 through 66 )
18X-RAY DIFFRACTION18chain 'D' and (resid 67 through 94 )
19X-RAY DIFFRACTION19chain 'D' and (resid 95 through 106 )
20X-RAY DIFFRACTION20chain 'D' and (resid 107 through 118 )
21X-RAY DIFFRACTION21chain 'D' and (resid 119 through 136 )
22X-RAY DIFFRACTION22chain 'D' and (resid 137 through 145 )
23X-RAY DIFFRACTION23chain 'D' and (resid 146 through 155 )
24X-RAY DIFFRACTION24chain 'D' and (resid 156 through 163 )
25X-RAY DIFFRACTION25chain 'D' and (resid 164 through 170 )
26X-RAY DIFFRACTION26chain 'E' and (resid 50 through 54 )
27X-RAY DIFFRACTION27chain 'E' and (resid 55 through 59 )
28X-RAY DIFFRACTION28chain 'E' and (resid 60 through 69 )
29X-RAY DIFFRACTION29chain 'E' and (resid 70 through 74 )
30X-RAY DIFFRACTION30chain 'E' and (resid 75 through 79 )
31X-RAY DIFFRACTION31chain 'E' and (resid 80 through 87 )
32X-RAY DIFFRACTION32chain 'F' and (resid 17 through 79 )
33X-RAY DIFFRACTION33chain 'F' and (resid 80 through 170 )
34X-RAY DIFFRACTION34chain 'G' and (resid 50 through 54 )
35X-RAY DIFFRACTION35chain 'G' and (resid 55 through 59 )
36X-RAY DIFFRACTION36chain 'G' and (resid 60 through 69 )
37X-RAY DIFFRACTION37chain 'G' and (resid 70 through 74 )
38X-RAY DIFFRACTION38chain 'G' and (resid 75 through 79 )
39X-RAY DIFFRACTION39chain 'G' and (resid 80 through 84 )
40X-RAY DIFFRACTION40chain 'G' and (resid 85 through 87 )
41X-RAY DIFFRACTION41chain 'H' and (resid 17 through 34 )
42X-RAY DIFFRACTION42chain 'H' and (resid 35 through 53 )
43X-RAY DIFFRACTION43chain 'H' and (resid 54 through 66 )
44X-RAY DIFFRACTION44chain 'H' and (resid 67 through 79 )
45X-RAY DIFFRACTION45chain 'H' and (resid 80 through 118 )
46X-RAY DIFFRACTION46chain 'H' and (resid 119 through 136 )
47X-RAY DIFFRACTION47chain 'H' and (resid 137 through 170 )

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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