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- PDB-4ptg: Structure of a carboxamine compound (26) (2-{2-[(CYCLOPROPYLCARBO... -

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基本情報

登録情報
データベース: PDB / ID: 4ptg
タイトルStructure of a carboxamine compound (26) (2-{2-[(CYCLOPROPYLCARBONYL)AMINO]PYRIDIN-4-YL}-4-METHOXYPYRIMIDINE-5-CARBOXAMIDE) to GSK3b
要素Glycogen synthase kinase-3 beta
キーワードtransferase/transferase inhibitor / Serine/threonine kinase / transferase-transferase inhibitor complex
機能・相同性
機能・相同性情報


neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation ...neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / beta-catenin destruction complex / CRMPs in Sema3A signaling / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / heart valve development / tau-protein kinase / regulation of microtubule-based process / regulation of protein export from nucleus / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Maturation of nucleoprotein / cellular response to interleukin-3 / regulation of long-term synaptic potentiation / Wnt signalosome / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / Maturation of nucleoprotein / G protein-coupled dopamine receptor signaling pathway / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / positive regulation of cell-matrix adhesion / regulation of axonogenesis / regulation of dendrite morphogenesis / ER overload response / glycogen metabolic process / regulation of neuron projection development / establishment of cell polarity / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / Regulation of HSF1-mediated heat shock response / negative regulation of osteoblast differentiation / epithelial to mesenchymal transition / canonical Wnt signaling pathway / NF-kappaB binding / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cellular response to heat / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / positive regulation of autophagy / presynaptic modulation of chemical synaptic transmission / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of microtubule cytoskeleton organization / response to endoplasmic reticulum stress / negative regulation of cell migration / hippocampus development / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / excitatory postsynaptic potential / mitochondrion organization / Ubiquitin-dependent degradation of Cyclin D / positive regulation of cell differentiation / positive regulation of protein-containing complex assembly / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / regulation of circadian rhythm / beta-catenin binding / Degradation of beta-catenin by the destruction complex / B-WICH complex positively regulates rRNA expression / tau protein binding / Wnt signaling pathway / circadian rhythm / cellular response to amyloid-beta / positive regulation of protein catabolic process / neuron projection development / Regulation of RUNX2 expression and activity / kinase activity / positive regulation of protein binding / p53 binding / positive regulation of neuron apoptotic process / insulin receptor signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / presynapse
類似検索 - 分子機能
Glycogen synthase kinase 3, catalytic domain / : / 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 ...Glycogen synthase kinase 3, catalytic domain / : / 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
Chem-2WG / Glycogen synthase kinase-3 beta
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: 2.361 Å
データ登録者Lewis, H.A. / Sivaprakasam, P. / Kish, K. / Pokross, M. / Dubowchik, G.M.
引用ジャーナル: Bioorg.Med.Chem.Lett. / 年: 2015
タイトル: Discovery of new acylaminopyridines as GSK-3 inhibitors by a structure guided in-depth exploration of chemical space around a pyrrolopyridinone core.
著者: Sivaprakasam, P. / Han, X. / Civiello, R.L. / Jacutin-Porte, S. / Kish, K. / Pokross, M. / Lewis, H.A. / Ahmed, N. / Szapiel, N. / Newitt, J.A. / Baldwin, E.T. / Xiao, H. / Krause, C.M. / ...著者: Sivaprakasam, P. / Han, X. / Civiello, R.L. / Jacutin-Porte, S. / Kish, K. / Pokross, M. / Lewis, H.A. / Ahmed, N. / Szapiel, N. / Newitt, J.A. / Baldwin, E.T. / Xiao, H. / Krause, C.M. / Park, H. / Nophsker, M. / Lippy, J.S. / Burton, C.R. / Langley, D.R. / Macor, J.E. / Dubowchik, G.M.
履歴
登録2014年3月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年4月8日Provider: repository / タイプ: Initial release
改定 1.12015年6月10日Group: Database references
改定 1.22024年2月28日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)99,2164
ポリマ－98,5902
非ポリマー6272
水3,279182
1
A: Glycogen synthase kinase-3 beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)49,6082
ポリマ－49,2951
非ポリマー3131
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: Glycogen synthase kinase-3 beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)49,6082
ポリマ－49,2951
非ポリマー3131
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)81.197, 83.372, 177.416
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 Glycogen synthase kinase-3 beta / GSK-3 beta / Serine/threonine-protein kinase GSK3B


分子量: 49294.828 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GSK3B
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: 化合物 ChemComp-2WG / 2-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}-4-methoxypyrimidine-5-carboxamide


分子量: 313.311 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C15H15N5O3
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 182 / 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: 3.05 Å3/Da / 溶媒含有率: 59.61 %
結晶化温度: 293 K / 手法: 蒸気拡散法
詳細: GSK-3 was mixed with a 10-fold molar excess of compound (1 mM final concentration). Crystals were grown at 20 C by vapor diffusion in the presence of 22% PEG 3350 and 3.0% w/v methanol. ...詳細: GSK-3 was mixed with a 10-fold molar excess of compound (1 mM final concentration). Crystals were grown at 20 C by vapor diffusion in the presence of 22% PEG 3350 and 3.0% w/v methanol. Crystals would nucleate within 1-3 days and continued to grow for an addition 5-10 days before harvesting., VAPOR DIFFUSION, temperature 293K

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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: 17-ID / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2011年7月21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: 2.36→94.7809 Å / Num. obs: 49754

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解析

ソフトウェア名称: PHENIX / バージョン: (phenix.refine: 1.8.4_1496) / 分類: 精密化
精密化構造決定の手法: 分子置換 / 解像度: 2.361→47.803 Å / SU ML: 0.27 / σ(F): 1.35 / 位相誤差: 22.61 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.211 2521 5.08 %Random
Rwork0.171 ---
obs0.173 49645 98.69 %-
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: 2.361→47.803 Å
タンパク質核酸リガンド溶媒全体
原子数5033 0 46 182 5261
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0075211
X-RAY DIFFRACTIONf_angle_d0.9477127
X-RAY DIFFRACTIONf_dihedral_angle_d11.8481831
X-RAY DIFFRACTIONf_chiral_restr0.037831
X-RAY DIFFRACTIONf_plane_restr0.005911
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3605-2.40590.34151400.23892557X-RAY DIFFRACTION98
2.4059-2.4550.25271740.21652530X-RAY DIFFRACTION98
2.455-2.50840.26251420.19792559X-RAY DIFFRACTION99
2.5084-2.56680.24431540.19292565X-RAY DIFFRACTION99
2.5668-2.63090.24981370.1882572X-RAY DIFFRACTION98
2.6309-2.70210.25391430.18372585X-RAY DIFFRACTION98
2.7021-2.78160.27981240.17982597X-RAY DIFFRACTION99
2.7816-2.87130.251270.18232605X-RAY DIFFRACTION99
2.8713-2.9740.25321510.19212575X-RAY DIFFRACTION99
2.974-3.0930.23641290.18412622X-RAY DIFFRACTION99
3.093-3.23370.24381370.18812599X-RAY DIFFRACTION99
3.2337-3.40420.21621310.18492632X-RAY DIFFRACTION99
3.4042-3.61740.22021450.18342622X-RAY DIFFRACTION99
3.6174-3.89660.23111340.16362632X-RAY DIFFRACTION99
3.8966-4.28850.16681320.14732663X-RAY DIFFRACTION99
4.2885-4.90850.18741300.13052682X-RAY DIFFRACTION99
4.9085-6.18210.1691270.16282711X-RAY DIFFRACTION99
6.1821-47.81320.17251640.17392816X-RAY DIFFRACTION99
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)
15.51340.96530.19316.0636-0.97733.7689-0.1311-0.0716-0.10180.6770.01440.70830.059-0.16970.18860.5658-0.10130.04930.2668-0.01680.555-7.3282-15.048141.5316
25.50960.5919-0.49462.3178-1.02133.3101-0.11010.4493-0.0054-0.18240.02990.07730.2717-0.14810.07380.4872-0.03350.01440.19530.02620.45690.5829-8.190434.9853
35.63984.3593.21633.60222.07043.13840.0347-0.2292-0.19590.0379-0.1513-0.05260.3333-0.03350.25870.55940.05940.05880.29370.0320.46552.9657-9.506143.5117
43.651.7147-0.86556.33580.73742.089-0.42480.22970.0305-0.41120.04040.5322-0.1806-0.24240.25960.4989-0.00830.05520.34480.0020.38010.7254-5.231236.0916
52.56022.2723-0.03684.0358-0.18424.1256-0.31020.12410.60520.24010.43240.6773-0.62270.1719-0.14240.55090.0553-0.01180.33730.09530.48119.814317.136736.7102
61.3809-0.2127-0.75071.7180.4473.1934-0.0598-0.0319-0.0444-0.149-0.0537-0.05740.2610.20270.13410.45170.04940.03030.29830.02630.345414.21230.406943.5113
72.24450.6388-1.48992.36021.8153.6966-0.0567-0.0603-0.1078-0.17690.0853-0.09380.22740.49-0.02120.49560.06560.01410.4210.05030.341424.9487-0.721234.301
82.8274-1.3245-1.60563.39551.3664.3030.24470.46070.1192-0.3764-0.12010.0198-0.8680.1375-0.21510.5283-0.02340.04180.51210.06010.423127.980510.331228.537
92.24052.64520.36318.889-1.58833.33540.0943-0.532-0.9652-1.0206-1.0406-1.55070.87170.30760.59450.57320.196-0.01661.05510.22060.737840.24331.893334.1503
105.84361.5975-0.56341.43881.32352.30160.3641-0.2720.0212-0.30960.9180.3748-0.087-0.5998-1.29491.2638-0.27780.28341.0614-0.04291.00239.157614.082331.4738
110.93322.23170.89495.84151.5985.01970.28310.0360.514-0.78030.0028-0.6289-1.40881.3461-0.4380.9053-0.185-0.02270.57780.04460.551426.960720.350641.6292
125.20292.19320.46098.59633.16174.0785-0.1495-1.10390.6808-1.04310.3518-0.0404-0.4730.5849-0.01510.4472-0.1325-0.09560.5998-0.01330.489627.868112.208446.0904
131.8773-0.5114-0.97713.18870.70334.58-0.2486-0.36250.10730.52280.1910.1826-0.15690.68440.03470.4643-0.0248-0.0350.36970.03970.401220.89348.430551.3446
143.08181.6081.83485.0374-3.34735.483-0.3062-0.5774-0.24081.3592-0.00950.59270.1976-0.37120.15840.56470.04130.03140.31530.03230.345810.92623.433957.4633
158.12682.848-2.07857.20770.10046.9321-0.5636-0.2097-0.6914-0.447-0.1024-0.79870.93250.23260.6050.78850.17290.0410.36560.04670.364921.195-6.979656.1249
165.6579-0.9704-1.68054.6895-1.31772.3565-0.5765-1.35780.56720.97020.3461-0.1694-0.28450.91420.25290.5215-0.0164-0.10620.72680.11450.313823.77630.417161.1433
178.2884-2.7548-1.46375.1629-0.14538.4704-0.5808-0.8830.98961.26570.52250.0621-0.84340.19330.23650.67610.1385-0.05880.69650.0160.334415.14785.805365.2965
185.3536-1.4854-1.69153.6492-0.10822.8189-0.17680.54860.7295-0.52590.2827-1.29330.37350.3910.13310.4673-0.22470.06780.4984-0.03490.679342.987726.26993.2544
199.45290.4931-0.29474.2124-0.16030.09770.65260.01621.16170.5049-0.14120.1974-0.84790.0106-0.10020.4066-0.07850.07680.541-0.09630.510731.2629.58159.4475
207.4170.17451.52139.338-4.53848.7053-0.0918-1.34270.3350.55290.0911-0.65390.23550.6803-0.25810.30990.08610.04740.69030.01040.47628.774522.670514.4041
216.6768-0.35072.75964.99161.43242.14750.2751-0.83610.4349-0.4768-0.0145-0.5545-0.67750.9144-0.0347-0.0156-0.04260.04470.75150.02840.441535.572622.710510.1669
225.88795.0261-1.56854.2743-1.44812.64890.55850.86460.1674-0.03250.84720.28980.02430.5466-1.03060.29210.06770.08330.7339-0.02760.639139.050511.57498.4178
235.62973.45612.33696.70852.93242.557-0.39510.22510.223-0.58720.5763-0.3467-0.56920.7746-0.28890.3294-0.06150.08880.6157-0.04510.40736.628417.4173.6489
245.27650.46390.19053.2970.35242.46050.3371-0.5320.58630.2909-0.35610.1139-0.14620.00430.05340.3243-0.03810.03550.42480.05050.280531.188321.149110.0353
252.54690.4905-2.08254.74361.6256.7450.28510.44020.61170.1959-0.32710.6560.3153-1.24530.05960.32660.07520.00060.5773-0.02930.55588.389612.08247.2037
261.2105-0.21790.82121.5491-0.17133.82470.0508-0.0109-0.0496-0.2556-0.1956-0.06980.24660.26840.11880.37250.09590.04020.472-0.00250.385824.88754.07821.3951
272.02090.77340.06952.6268-0.43186.6568-0.1347-0.03050.4312-0.0719-0.1796-0.0234-0.6146-0.08180.11580.28570.06670.01830.42860.0460.404720.577613.54162.2093
281.6639-1.05151.21134.314-0.49922.67510.0192-0.09760.0163-0.1766-0.3181-0.5819-0.3190.7212-0.08020.26540.13350.04420.71370.08330.442835.07764.477910.1947
292.0037-1.2321-0.09844.11871.09441.12810.1288-0.34750.4599-0.0849-0.0179-0.72410.55290.66450.01490.38840.2694-0.03590.74720.05650.395635.1058-2.889717.2072
301.85520.61230.54642.8291-0.5174.477-0.1129-0.141-0.17690.4865-0.0878-0.15730.63370.42940.08280.51290.08940.01290.44440.01950.422826.0483-4.72616.7656
311.747-0.38541.63672.802-0.50314.0628-0.12540.1725-0.3911-0.1074-0.13290.15840.5170.04720.1030.36240.04690.03750.3625-0.00780.315718.9533-0.87047.814
321.6538-0.29941.51511.5361-1.47634.9913-0.1856-0.1469-0.19650.6410.12340.12450.1469-0.5210.16890.45110.04750.02190.4586-0.01860.393812.7121-0.167217.4074
332.84810.27470.64682.86260.20475.5386-0.4102-0.4330.08360.37090.00340.66610.1863-0.69780.07080.5351-0.01630.0840.46020.00380.478914.2047-8.367419.21
346.71561.9255-0.89523.9081-0.56182.7838-0.8294-0.8088-0.6176-0.5040.13160.06431.04271.10180.63381.30430.32240.04180.59170.11260.773422.349-17.981815.38
356.0831-2.80180.27783.58140.83690.42580.9935-0.4926-1.61491.5575-0.73090.72681.2469-1.3311-0.03760.9258-0.2931-0.07190.9955-0.09380.63776.8027-10.89698.4357
365.59363.38240.26353.98440.28238.41490.1715-0.2323-1.2795-0.69770.08240.92150.9369-1.3128-0.04270.5248-0.141-0.05870.4855-0.07820.562310.2679-5.83641.2153
373.77390.15370.15081.86541.34584.22350.05310.6724-0.008-0.3981-0.21630.2240.3240.16950.21880.46230.11750.00570.4389-0.03340.351822.2033-0.4153-7.0205
382.93311.06230.4895.4462-3.42892.65550.0981.09310.2382-1.20371.10730.0655-0.3894-1.2615-1.18350.83390.1520.04550.9351-0.01120.397824.12572.8833-20.8184
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 154 )
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 208 )
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 252 )
8X-RAY DIFFRACTION8chain 'A' and (resid 253 through 273 )
9X-RAY DIFFRACTION9chain 'A' and (resid 274 through 284 )
10X-RAY DIFFRACTION10chain 'A' and (resid 293 through 300 )
11X-RAY DIFFRACTION11chain 'A' and (resid 301 through 310 )
12X-RAY DIFFRACTION12chain 'A' and (resid 311 through 320 )
13X-RAY DIFFRACTION13chain 'A' and (resid 321 through 354 )
14X-RAY DIFFRACTION14chain 'A' and (resid 355 through 363 )
15X-RAY DIFFRACTION15chain 'A' and (resid 364 through 370 )
16X-RAY DIFFRACTION16chain 'A' and (resid 371 through 377 )
17X-RAY DIFFRACTION17chain 'A' and (resid 378 through 382 )
18X-RAY DIFFRACTION18chain 'B' and (resid 37 through 51 )
19X-RAY DIFFRACTION19chain 'B' and (resid 52 through 64 )
20X-RAY DIFFRACTION20chain 'B' and (resid 65 through 74 )
21X-RAY DIFFRACTION21chain 'B' and (resid 75 through 95 )
22X-RAY DIFFRACTION22chain 'B' and (resid 96 through 101 )
23X-RAY DIFFRACTION23chain 'B' and (resid 102 through 119 )
24X-RAY DIFFRACTION24chain 'B' and (resid 124 through 138 )
25X-RAY DIFFRACTION25chain 'B' and (resid 139 through 154 )
26X-RAY DIFFRACTION26chain 'B' and (resid 155 through 183 )
27X-RAY DIFFRACTION27chain 'B' and (resid 184 through 198 )
28X-RAY DIFFRACTION28chain 'B' and (resid 199 through 208 )
29X-RAY DIFFRACTION29chain 'B' and (resid 209 through 218 )
30X-RAY DIFFRACTION30chain 'B' and (resid 219 through 235 )
31X-RAY DIFFRACTION31chain 'B' and (resid 236 through 252 )
32X-RAY DIFFRACTION32chain 'B' and (resid 253 through 261 )
33X-RAY DIFFRACTION33chain 'B' and (resid 262 through 273 )
34X-RAY DIFFRACTION34chain 'B' and (resid 274 through 284 )
35X-RAY DIFFRACTION35chain 'B' and (resid 298 through 304 )
36X-RAY DIFFRACTION36chain 'B' and (resid 305 through 320 )
37X-RAY DIFFRACTION37chain 'B' and (resid 321 through 377 )
38X-RAY DIFFRACTION38chain 'B' and (resid 378 through 385 )

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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