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- PDB-6oyt: ASK1 kinase domain in complex with GS-4997 -

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基本情報

登録情報
データベース: PDB / ID: 6oyt
タイトルASK1 kinase domain in complex with GS-4997
要素Mitogen-activated protein kinase kinase kinase 5
キーワードTransferase/Transferase Inhibitor / ASK1 MAP3K5 / Transferase-Transferase Inhibitor complex
機能・相同性
機能・相同性情報


cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress ...cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress / p38MAPK cascade / positive regulation of JUN kinase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / MAP kinase kinase kinase activity / positive regulation of myoblast differentiation / positive regulation of cardiac muscle cell apoptotic process / stress-activated MAPK cascade / positive regulation of vascular associated smooth muscle cell proliferation / JNK cascade / cellular response to amino acid starvation / response to endoplasmic reticulum stress / response to ischemia / positive regulation of JNK cascade / apoptotic signaling pathway / cellular response to hydrogen peroxide / cellular senescence / MAPK cascade / cellular response to tumor necrosis factor / Oxidative Stress Induced Senescence / protein phosphatase binding / neuron apoptotic process / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / innate immune response / external side of plasma membrane / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm
類似検索 - 分子機能
MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / Sterile alpha motif/pointed domain superfamily / Phosphorylase Kinase; domain 1 ...MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / Sterile alpha motif/pointed domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
ACETATE ION / Chem-NJV / Mitogen-activated protein kinase kinase kinase 5
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: 2.824 Å
データ登録者Marcotte, D.J.
引用ジャーナル: J.Med.Chem. / 年: 2019
タイトル: Rational Design and Optimization of a Novel Class of Macrocyclic Apoptosis Signal-Regulating Kinase 1 Inhibitors.
著者: Himmelbauer, M.K. / Xin, Z. / Jones, J.H. / Enyedy, I. / King, K. / Marcotte, D.J. / Murugan, P. / Santoro, J.C. / Hesson, T. / Spilker, K. / Johnson, J.L. / Luzzio, M.J. / Gilfillan, R. / de Turiso, F.G.
履歴
登録2019年5月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年11月27日Provider: repository / タイプ: Initial release
改定 1.12019年12月4日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22019年12月25日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年10月11日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Mitogen-activated protein kinase kinase kinase 5
B: Mitogen-activated protein kinase kinase kinase 5
C: Mitogen-activated protein kinase kinase kinase 5
D: Mitogen-activated protein kinase kinase kinase 5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)129,12217
ポリマ－126,8084
非ポリマー2,31313
水1,42379
1
A: Mitogen-activated protein kinase kinase kinase 5
C: Mitogen-activated protein kinase kinase kinase 5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)64,4136
ポリマ－63,4042
非ポリマー1,0094
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-9 kcal/mol
Surface area20590 Å2
手法PISA
2
B: Mitogen-activated protein kinase kinase kinase 5
D: Mitogen-activated protein kinase kinase kinase 5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)64,70911
ポリマ－63,4042
非ポリマー1,3049
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-11 kcal/mol
Surface area22080 Å2
手法PISA
単位格子
Length a, b, c (Å)86.510, 73.590, 95.140
Angle α, β, γ (deg.)90.000, 97.770, 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 671 through 672 and (name N...
21(chain B and ((resid 671 through 672 and (name N...
31(chain C and (resid 671 through 687 or (resid 688...
41(chain D and ((resid 671 through 672 and (name N...

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
11LEULEUGLUGLU(chain A and ((resid 671 through 672 and (name N...AA671 - 6726 - 7
12METMETLYSLYS(chain A and ((resid 671 through 672 and (name N...AA666 - 9391 - 274
13METMETLYSLYS(chain A and ((resid 671 through 672 and (name N...AA666 - 9391 - 274
14METMETLYSLYS(chain A and ((resid 671 through 672 and (name N...AA666 - 9391 - 274
15METMETLYSLYS(chain A and ((resid 671 through 672 and (name N...AA666 - 9391 - 274
21LEULEUGLUGLU(chain B and ((resid 671 through 672 and (name N...BB671 - 6726 - 7
22LEULEULYSLYS(chain B and ((resid 671 through 672 and (name N...BB670 - 9395 - 274
23LEULEULYSLYS(chain B and ((resid 671 through 672 and (name N...BB670 - 9395 - 274
24LEULEULYSLYS(chain B and ((resid 671 through 672 and (name N...BB670 - 9395 - 274
25LEULEULYSLYS(chain B and ((resid 671 through 672 and (name N...BB670 - 9395 - 274
31LEULEUGLYGLY(chain C and (resid 671 through 687 or (resid 688...CC671 - 6876 - 22
32LYSLYSLYSLYS(chain C and (resid 671 through 687 or (resid 688...CC68823
33LEULEULEULEU(chain C and (resid 671 through 687 or (resid 688...CC671 - 9386 - 273
34LEULEULEULEU(chain C and (resid 671 through 687 or (resid 688...CC671 - 9386 - 273
35LEULEULEULEU(chain C and (resid 671 through 687 or (resid 688...CC671 - 9386 - 273
36LEULEULEULEU(chain C and (resid 671 through 687 or (resid 688...CC671 - 9386 - 273
41LEULEUGLUGLU(chain D and ((resid 671 through 672 and (name N...DD671 - 6726 - 7
42METMETACTACT(chain D and ((resid 671 through 672 and (name N...DD - M666 - 10011
43METMETACTACT(chain D and ((resid 671 through 672 and (name N...DD - M666 - 10011
44METMETACTACT(chain D and ((resid 671 through 672 and (name N...DD - M666 - 10011
45METMETACTACT(chain D and ((resid 671 through 672 and (name N...DD - M666 - 10011

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要素

#1: タンパク質
Mitogen-activated protein kinase kinase kinase 5 / Apoptosis signal-regulating kinase 1 / ASK-1 / MAPK/ERK kinase kinase 5 / MEKK 5


分子量: 31702.111 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MAP3K5, ASK1, MAPKKK5, MEKK5 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q99683, mitogen-activated protein kinase kinase kinase
#2: 化合物
ChemComp-NJV / 5-(4-cyclopropyl-1H-imidazol-1-yl)-2-fluoro-4-methyl-N-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}benzamide / Selonsertib / GS-4997


分子量: 445.492 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C24H24FN7O
#3: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C2H3O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 79 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.37 Å3/Da / 溶媒含有率: 48.02 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.1M Na Acetate pH 5.5, 2% PEG4K and 30% polyacrylic acid.

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
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: 1 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2016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: 1 Å / 相対比: 1
反射解像度: 2.82→50 Å / Num. obs: 51795 / % possible obs: 92.8 % / 冗長度: 1.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.4
反射 シェル解像度: 2.82→2.98 Å / Rmerge(I) obs: 0.78 / Num. unique obs: 7763 / CC1/2: 0.572 / % possible all: 86

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
Aimlessデータスケーリング
PDB_EXTRACT3.25データ抽出
MOSFLM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: 4BF2

4bf2


解像度: 2.824→47.133 Å / SU ML: 0.39 / 交差検証法: THROUGHOUT / σ(F): 1.37 / 位相誤差: 30.83 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2896 1397 5 %
Rwork0.2321 26545 -
obs0.2349 27942 97.36 %
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: 191.55 Å2 / Biso mean: 74.0106 Å2 / Biso min: 15.97 Å2
精密化ステップサイクル: final / 解像度: 2.824→47.133 Å
タンパク質核酸リガンド溶媒全体
原子数7309 0 168 79 7556
Biso mean--49.07 50.17 -
残基数----949
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2525X-RAY DIFFRACTION6.122TORSIONAL
12B2525X-RAY DIFFRACTION6.122TORSIONAL
13C2525X-RAY DIFFRACTION6.122TORSIONAL
14D2525X-RAY DIFFRACTION6.122TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.824-2.9250.38451270.34082419254689
2.925-3.04210.36431390.30742642278198
3.0421-3.18050.32061390.2812648278798
3.1805-3.34810.2761410.26582675281698
3.3481-3.55780.27971400.24612647278799
3.5578-3.83240.29811400.22512675281599
3.8324-4.21790.25811420.20412686282899
4.2179-4.82770.23921420.18622703284599
4.8277-6.08030.28081420.21832705284799
6.0803-47.13950.31871450.23182745289098
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)
15.93.0555-1.63812.6182-0.07687.01630.081-0.46950.1018-0.11310.14240.14630.4674-0.9181-0.20930.46890.0879-0.07210.4190.00780.3345-0.3526-23.383116.3951
29.424.28610.86684.72141.69186.95140.13860.5929-0.7419-0.05010.1186-0.4590.4765-0.7069-0.17740.4435-0.0345-0.0370.29130.090.3078-0.7645-20.39615.0799
35.8251-3.73480.01712.0037-2.73241.5919-1.02030.0353-0.5603-2.48570.67591.8279-0.2587-1.12140.1881.10240.3749-0.19421.06240.02950.5156-13.1638-11.62189.3134
45.5240.04361.5323.49850.23143.9901-0.27630.00710.406-0.7154-0.1080.0481-0.9114-0.94740.32370.48660.0342-0.01070.43040.07140.3253-4.9246-13.686813.7839
54.5066-1.94020.62586.70110.86632.2510.0048-0.3230.50120.1716-0.43970.1904-0.6442-0.66410.28520.73730.2483-0.00740.92-0.11060.3996-10.7521-7.284333.3396
65.3078-0.45320.55574.2876-0.02562.31520.3182-0.01910.1608-0.1762-0.03920.6974-0.3545-1.1501-0.09520.65270.3216-0.01470.826-0.040.4947-11.2371-9.136724.9795
75.4609-3.705-1.38378.5533-2.89012.7780.52990.5542-0.05143.7596-0.4872.1519-0.9814-0.35060.44710.70250.08340.47630.8945-0.2030.804-19.8579-9.445816.5524
85.2937-1.51032.10562.81330.24414.87150.314-1.1664-0.4120.11021.03671.0008-0.3103-2.9064-0.84550.54790.2379-0.03171.40780.02250.8765-20.6403-8.408631.9623
96.596-2.63380.42365.5092-1.47884.1380.7514-0.30710.2421.7535-1.73151.07970.40640.66770.11551.101-0.10220.17391.06170.13920.6341-22.8694-11.430841.8783
105.5598-0.7382-4.18558.0907-1.88895.65951.1720.75870.6113-0.3634-0.32730.452-0.4111-0.7528-0.55720.73510.3017-0.0680.9171-0.04840.8271-23.32071.374234.3128
112.5749-1.55581.18635.47620.20956.2403-0.0542-1.096-0.38590.63560.4978-0.070.2525-0.1737-0.46210.3943-0.05280.0050.5770.00960.437513.510323.36336.7359
124.57510.1814-0.66763.1327-0.11985.4028-0.0681-0.90510.99190.57110.0837-0.7004-0.66510.5330.02510.51550.1014-0.14880.5641-0.20810.760420.732332.804633.1089
134.70420.6420.50683.4542-2.32785.46390.05840.6190.2632-0.28140.0949-0.7474-0.06740.408-0.15920.2896-0.0120.07150.3451-0.03030.563423.95925.472915.639
145.40280.1757-0.29620.5027-0.94964.7827-0.7470.0801-0.374-0.2870.5285-0.56080.21241.075-0.13980.6619-0.1846-0.03590.8606-0.11820.967236.407129.159623.4975
155.71390.36632.17984.97980.6463.84930.08151.08990.707-0.49-0.1876-1.1189-0.1041.29660.02780.4838-0.1180.170.8885-0.01781.0136.477924.86539.1933
162.26831.6778-0.61454.34472.45946.0338-0.0259-0.8975-0.26911.11960.17230.03970.8965-0.08090.17850.82980.07140.06450.7937-0.03960.52556.2771-14.83146.6201
177.15360.9576-1.50934.1546-0.96451.3646-0.3929-1.2808-0.75561.5835-0.3164-1.1774-0.8461-0.1302-0.03380.67350.2494-0.07540.8372-0.29920.115912.6967-8.543343.068
184.41240.6326-1.98650.9163-1.09771.5461-1.0198-2.32160.7549-0.3823-0.1476-0.8282-0.53380.80960.05731.12920.1305-0.2820.9512-0.36990.965723.27250.75442.6618
195.178-0.24180.77022.38280.8376.2104-0.36860.02780.45110.08310.2042-0.2939-0.65720.52230.04390.43310.0059-0.02640.2033-0.00490.355717.4774-7.037927.8314
204.7352-1.6216-1.41152.7599-0.15864.3344-0.1779-0.03791.09650.18380.2171-2.2446-0.22861.7868-0.04480.907-0.0851-0.16861.1492-0.06610.922634.1725-4.510231.0552
216.2151-1.5917-0.57233.94290.55077.1585-0.12530.62520.35510.26190.4314-0.465-0.57571.4026-0.08470.4519-0.07950.13040.79980.01020.58929.2933-10.191821.4305
221.06730.13050.39370.46270.46063.63290.5011.3793-1.39750.04030.719-0.5398-0.63292.3333-0.09850.64860.15150.01071.2551-0.02111.262531.531-19.146815.655
234.39620.24430.72823.8897-0.07722.7802-0.41441.55661.6188-1.70280.1994-1.3188-0.6521.7599-0.00630.8013-0.29250.161.1293-0.08580.969131.4686-4.777113.1243
247.17230.9413-2.60051.40320.36985.53980.31841.146-1.32980.46860.0168-0.49730.450.0873-0.07070.60450.1172-0.06420.248-0.0480.42892.519814.55068.0966
253.2286-2.7132-1.42967.81817.62868.9345-0.09410.59320.1568-0.4728-0.5530.606-0.1851-0.15730.59980.3456-0.0260.06860.33290.04720.4138-4.4626.47214.9579
266.4717-0.83080.87395.3772-1.63215.76530.05290.1898-0.4545-1.4824-0.3277-0.04920.91680.0217-0.23830.3562-0.05130.04170.30520.10590.3571-0.302217.92156.8376
273.3974-1.05861.34183.7345-0.18346.2636-0.1091-0.36010.0890.37280.326-0.00070.3548-0.5774-0.19810.2751-0.05480.08520.2957-0.00470.2132-6.041328.802323.695
283.5050.4028-0.70384.8677-1.88666.47790.92620.2578-1.30580.06310.56890.97360.6165-0.9694-0.94560.6463-0.1796-0.01550.47780.07690.5482-13.393226.307414.3673
295.9392-2.00840.55595.1773-2.11282.21190.53910.573-1.3045-0.49880.11240.82661.2914-0.3763-0.27440.4491-0.11380.04220.5322-0.0250.4167-18.781429.052322.5458
307.2181-2.99751.11832.4329-0.3970.35821.8241-0.73450.2069-0.6963-1.39630.4160.3506-1.011-0.4671.007-0.2551-0.15050.9275-0.17910.7417-23.761219.270227.6562
314.3887-3.43162.46233.718-1.73996.0312-0.3785-0.9911-0.27320.12270.83460.5728-0.0964-1.4543-0.42560.422-0.06640.1040.62710.13530.3995-20.657934.819530.5856
329.4689-1.9829-6.33622.9264-2.22189.57420.4889-1.00471.13750.2903-0.0420.0225-0.8125-0.7158-0.2090.4873-0.01010.02650.3401-0.05190.4754-9.770142.960528.5293
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 666 through 692 )A666 - 692
2X-RAY DIFFRACTION2chain 'A' and (resid 693 through 720 )A693 - 720
3X-RAY DIFFRACTION3chain 'A' and (resid 721 through 731 )A721 - 731
4X-RAY DIFFRACTION4chain 'A' and (resid 732 through 758 )A732 - 758
5X-RAY DIFFRACTION5chain 'A' and (resid 759 through 796 )A759 - 796
6X-RAY DIFFRACTION6chain 'A' and (resid 797 through 820 )A797 - 820
7X-RAY DIFFRACTION7chain 'A' and (resid 821 through 859 )A821 - 859
8X-RAY DIFFRACTION8chain 'A' and (resid 860 through 876 )A860 - 876
9X-RAY DIFFRACTION9chain 'A' and (resid 877 through 908 )A877 - 908
10X-RAY DIFFRACTION10chain 'A' and (resid 909 through 939 )A909 - 939
11X-RAY DIFFRACTION11chain 'B' and (resid 670 through 703 )B670 - 703
12X-RAY DIFFRACTION12chain 'B' and (resid 704 through 758 )B704 - 758
13X-RAY DIFFRACTION13chain 'B' and (resid 759 through 820 )B759 - 820
14X-RAY DIFFRACTION14chain 'B' and (resid 821 through 859 )B821 - 859
15X-RAY DIFFRACTION15chain 'B' and (resid 860 through 939 )B860 - 939
16X-RAY DIFFRACTION16chain 'C' and (resid 671 through 684 )C671 - 684
17X-RAY DIFFRACTION17chain 'C' and (resid 685 through 715 )C685 - 715
18X-RAY DIFFRACTION18chain 'C' and (resid 716 through 731 )C716 - 731
19X-RAY DIFFRACTION19chain 'C' and (resid 732 through 820 )C732 - 820
20X-RAY DIFFRACTION20chain 'C' and (resid 821 through 859 )C821 - 859
21X-RAY DIFFRACTION21chain 'C' and (resid 860 through 876 )C860 - 876
22X-RAY DIFFRACTION22chain 'C' and (resid 877 through 908 )C877 - 908
23X-RAY DIFFRACTION23chain 'C' and (resid 909 through 938 )C909 - 938
24X-RAY DIFFRACTION24chain 'D' and (resid 666 through 720 )D666 - 720
25X-RAY DIFFRACTION25chain 'D' and (resid 721 through 746 )D721 - 746
26X-RAY DIFFRACTION26chain 'D' and (resid 747 through 758 )D747 - 758
27X-RAY DIFFRACTION27chain 'D' and (resid 759 through 817 )D759 - 817
28X-RAY DIFFRACTION28chain 'D' and (resid 818 through 845 )D818 - 845
29X-RAY DIFFRACTION29chain 'D' and (resid 846 through 876 )D846 - 876
30X-RAY DIFFRACTION30chain 'D' and (resid 877 through 896 )D877 - 896
31X-RAY DIFFRACTION31chain 'D' and (resid 897 through 928 )D897 - 928
32X-RAY DIFFRACTION32chain 'D' and (resid 929 through 941 )D929 - 941

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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