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- PDB-6uwy: DYRK1A bound to a harmine derivative -

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基本情報

登録情報
データベース: PDB / ID: 6uwy
タイトルDYRK1A bound to a harmine derivative
要素Dual specificity tyrosine-phosphorylation-regulated kinase 1ADYRK1A
キーワードTRANSFERASE/TRANSFERASE INHIBITOR / kinase (キナーゼ) / TRANSFERASE (転移酵素) / TRANSFERASE-TRANSFERASE Inhibitor complex
機能・相同性
機能・相同性情報


histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / protein serine/threonine/tyrosine kinase activity / cytoskeletal protein binding / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / non-membrane spanning protein tyrosine kinase activity / tau protein binding / 概日リズム / peptidyl-tyrosine phosphorylation / : / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / 細胞骨格 / protein kinase activity / nuclear speck / ribonucleoprotein complex / 神経繊維 / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / 樹状突起 / positive regulation of DNA-templated transcription / 核質 / ATP binding / identical protein binding / 細胞核 / 細胞質
類似検索 - 分子機能
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / 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
類似検索 - ドメイン・相同性
Chem-QKG / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
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 / フーリエ合成 / 解像度: 2.95 Å
データ登録者Khamrui, S. / Lazarus, M.B.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124838 米国
引用ジャーナル: J.Med.Chem. / 年: 2020
タイトル: Synthesis and Biological Validation of a Harmine-Based, Central Nervous System (CNS)-Avoidant, Selective, Human beta-Cell Regenerative Dual-Specificity Tyrosine Phosphorylation- ...タイトル: Synthesis and Biological Validation of a Harmine-Based, Central Nervous System (CNS)-Avoidant, Selective, Human beta-Cell Regenerative Dual-Specificity Tyrosine Phosphorylation-Regulated Kinase A (DYRK1A) Inhibitor.
著者: Kumar, K. / Wang, P. / Wilson, J. / Zlatanic, V. / Berrouet, C. / Khamrui, S. / Secor, C. / Swartz, E.A. / Lazarus, M. / Sanchez, R. / Stewart, A.F. / Garcia-Ocana, A. / DeVita, R.J.
履歴
登録2019年11月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年2月12日Provider: repository / タイプ: Initial release
改定 1.12020年4月8日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
改定 1.22023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
改定 1.32023年11月15日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)171,65219
ポリマ－168,3264
非ポリマー3,32615
水19811
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,9625
ポリマ－42,0821
非ポリマー8804
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,9625
ポリマ－42,0821
非ポリマー8804
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,7674
ポリマ－42,0821
非ポリマー6863
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)42,9625
ポリマ－42,0821
非ポリマー8804
水0
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)264.042, 65.218, 138.758
Angle α, β, γ (deg.)90.000, 114.860, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 135 or (resid 136 and (name...
21(chain B and (resseq 135 or (resid 136 and (name...
31(chain C and (resseq 135 or (resid 136 and (name...
41(chain D and (resseq 135 or (resid 136 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
11VALVALVALVAL(chain A and (resseq 135 or (resid 136 and (name...AA13511
12TYRTYRTYRTYR(chain A and (resseq 135 or (resid 136 and (name...AA13612
13VALVALLYSLYS(chain A and (resseq 135 or (resid 136 and (name...AA135 - 48111 - 357
14VALVALLYSLYS(chain A and (resseq 135 or (resid 136 and (name...AA135 - 48111 - 357
15VALVALLYSLYS(chain A and (resseq 135 or (resid 136 and (name...AA135 - 48111 - 357
16VALVALLYSLYS(chain A and (resseq 135 or (resid 136 and (name...AA135 - 48111 - 357
17VALVALLYSLYS(chain A and (resseq 135 or (resid 136 and (name...AA135 - 48111 - 357
18VALVALLYSLYS(chain A and (resseq 135 or (resid 136 and (name...AA135 - 48111 - 357
19VALVALLYSLYS(chain A and (resseq 135 or (resid 136 and (name...AA135 - 48111 - 357
110VALVALLYSLYS(chain A and (resseq 135 or (resid 136 and (name...AA135 - 48111 - 357
111VALVALLYSLYS(chain A and (resseq 135 or (resid 136 and (name...AA135 - 48111 - 357
21VALVALVALVAL(chain B and (resseq 135 or (resid 136 and (name...BB13511
22TYRTYRTYRTYR(chain B and (resseq 135 or (resid 136 and (name...BB13612
23LYSLYSLYSLYS(chain B and (resseq 135 or (resid 136 and (name...BB134 - 48110 - 357
24LYSLYSLYSLYS(chain B and (resseq 135 or (resid 136 and (name...BB134 - 48110 - 357
25LYSLYSLYSLYS(chain B and (resseq 135 or (resid 136 and (name...BB134 - 48110 - 357
26LYSLYSLYSLYS(chain B and (resseq 135 or (resid 136 and (name...BB134 - 48110 - 357
27LYSLYSLYSLYS(chain B and (resseq 135 or (resid 136 and (name...BB134 - 48110 - 357
28LYSLYSLYSLYS(chain B and (resseq 135 or (resid 136 and (name...BB134 - 48110 - 357
29LYSLYSLYSLYS(chain B and (resseq 135 or (resid 136 and (name...BB134 - 48110 - 357
210LYSLYSLYSLYS(chain B and (resseq 135 or (resid 136 and (name...BB134 - 48110 - 357
211LYSLYSLYSLYS(chain B and (resseq 135 or (resid 136 and (name...BB134 - 48110 - 357
31VALVALVALVAL(chain C and (resseq 135 or (resid 136 and (name...CC13511
32TYRTYRTYRTYR(chain C and (resseq 135 or (resid 136 and (name...CC13612
33VALVALLYSLYS(chain C and (resseq 135 or (resid 136 and (name...CC135 - 48111 - 357
34VALVALLYSLYS(chain C and (resseq 135 or (resid 136 and (name...CC135 - 48111 - 357
35VALVALLYSLYS(chain C and (resseq 135 or (resid 136 and (name...CC135 - 48111 - 357
36VALVALLYSLYS(chain C and (resseq 135 or (resid 136 and (name...CC135 - 48111 - 357
37VALVALLYSLYS(chain C and (resseq 135 or (resid 136 and (name...CC135 - 48111 - 357
38VALVALLYSLYS(chain C and (resseq 135 or (resid 136 and (name...CC135 - 48111 - 357
39VALVALLYSLYS(chain C and (resseq 135 or (resid 136 and (name...CC135 - 48111 - 357
310VALVALLYSLYS(chain C and (resseq 135 or (resid 136 and (name...CC135 - 48111 - 357
311VALVALLYSLYS(chain C and (resseq 135 or (resid 136 and (name...CC135 - 48111 - 357
41VALVALVALVAL(chain D and (resseq 135 or (resid 136 and (name...DD13511
42TYRTYRTYRTYR(chain D and (resseq 135 or (resid 136 and (name...DD13612
43LYSLYSLYSLYS(chain D and (resseq 135 or (resid 136 and (name...DD134 - 48110 - 357
44LYSLYSLYSLYS(chain D and (resseq 135 or (resid 136 and (name...DD134 - 48110 - 357
45LYSLYSLYSLYS(chain D and (resseq 135 or (resid 136 and (name...DD134 - 48110 - 357
46LYSLYSLYSLYS(chain D and (resseq 135 or (resid 136 and (name...DD134 - 48110 - 357
47LYSLYSLYSLYS(chain D and (resseq 135 or (resid 136 and (name...DD134 - 48110 - 357
48LYSLYSLYSLYS(chain D and (resseq 135 or (resid 136 and (name...DD134 - 48110 - 357
49LYSLYSLYSLYS(chain D and (resseq 135 or (resid 136 and (name...DD134 - 48110 - 357
410LYSLYSLYSLYS(chain D and (resseq 135 or (resid 136 and (name...DD134 - 48110 - 357
411LYSLYSLYSLYS(chain D and (resseq 135 or (resid 136 and (name...DD134 - 48110 - 357

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要素

#1: タンパク質
Dual specificity tyrosine-phosphorylation-regulated kinase 1A / DYRK1A / Dual specificity YAK1-related kinase / HP86 / Protein kinase minibrain homolog / hMNB


分子量: 42081.535 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: DYRK1A, DYRK, MNB, MNBH / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: Q13627, dual-specificity kinase
#2: 化合物
ChemComp-QKG / 4-(7-methoxy-1-methyl-9H-beta-carbolin-9-yl)butanamide


分子量: 297.352 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C17H19N3O2 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-PG4 / TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル / ポリエチレングリコール


分子量: 194.226 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C8H18O5 / コメント: 沈殿剤*YM
#4: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 11 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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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: 3.22 Å3/Da / 溶媒含有率: 61.8 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.8
詳細: 35-45% PEG400, 0.2 M lithium sulfate, 0.1 M Tris, pH 8.8

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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: NSLS-II / ビームライン: 17-ID-1 / 波長: 0.920126 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2018年7月13日
放射モノクロメーター: Si(111) / 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: 0.920126 Å / 相対比: 1
反射解像度: 2.95→125.9 Å / Num. obs: 45687 / % possible obs: 100 % / 冗長度: 7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.081 / Rrim(I) all: 0.215 / Net I/σ(I): 7.5 / Num. measured all: 319025 / Scaling rejects: 5
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.95-3.057.32.6023203243970.3441.032.8010.999.9
11.43-125.96.60.06956568600.9950.0290.07522.199.8

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
Aimless0.7.1データスケーリング
PHENIX1.10.1_2155精密化
PDB_EXTRACT3.25データ抽出
PHENIX位相決定
精密化構造決定の手法: フーリエ合成
開始モデル: 4YLJ

4ylj


解像度: 2.95→119.8 Å / SU ML: 0.44 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 25.47
Rfactor反射数%反射
Rfree0.2271 2324 5.09 %
Rwork0.1951 --
obs0.1967 45665 99.91 %
溶媒の処理減衰半径: 0.8 Å / VDWプローブ半径: 1.1 Å
原子変位パラメータBiso max: 251.74 Å2 / Biso mean: 98.726 Å2 / Biso min: 40.54 Å2
精密化ステップサイクル: final / 解像度: 2.95→119.8 Å
タンパク質核酸リガンド溶媒全体
原子数11342 0 295 11 11648
Biso mean--96.77 52.77 -
残基数----1390
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00311906
X-RAY DIFFRACTIONf_angle_d0.68316036
X-RAY DIFFRACTIONf_chiral_restr0.0481671
X-RAY DIFFRACTIONf_plane_restr0.0032031
X-RAY DIFFRACTIONf_dihedral_angle_d16.9647138
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A6576X-RAY DIFFRACTION3.435TORSIONAL
12B6576X-RAY DIFFRACTION3.435TORSIONAL
13C6576X-RAY DIFFRACTION3.435TORSIONAL
14D6576X-RAY DIFFRACTION3.435TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.9501-3.01030.41151290.35642528
3.0103-3.07580.34781410.33032520
3.0758-3.14730.33261490.29742503
3.1473-3.22610.33551460.27752529
3.2261-3.31330.29381260.27222538
3.3133-3.41080.29861390.24942521
3.4108-3.52090.28511300.23642515
3.5209-3.64670.23481210.21882592
3.6467-3.79280.23681260.20032507
3.7928-3.96540.2461360.18342551
3.9654-4.17450.21421260.17362542
4.1745-4.4360.24111310.16932551
4.436-4.77850.17591410.14762560
4.7785-5.25940.20311380.15932551
5.2594-6.02040.2071620.18732572
6.0204-7.5850.1891480.18432573
7.585-119.780.17151350.16412688
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)
16.57650.2168-0.06385.8328-0.63123.99480.5262-0.44240.9251-0.4660.1925-0.8087-1.65281.2279-0.33651.6286-0.62290.40071.1002-0.02011.522420.459731.628926.4598
22.74710.32-0.54863.35860.33023.7627-0.038-0.2250.4392-0.04420.1641-1.422-0.76480.9536-0.28861.1982-0.34420.09561.241-0.24321.116320.689318.638330.6703
33.9349-0.28481.04284.2911-0.53816.2644-0.1631-0.73950.12780.68020.3176-1.389-1.140.3756-0.23541.1828-0.145-0.12021.1165-0.10730.917416.54869.991832.8753
43.6268-0.67120.5713.79381.05223.50060.1959-0.21270.36590.13190.1424-0.0728-1.01440.0818-0.21111.2132-0.258-0.0480.6331-0.05180.54733.140917.939432.3521
56.92411.0114-1.74881.3119-1.19432.9760.3608-1.384-0.2282.1228-0.10550.16361.3027-0.0952-0.03561.4408-0.2832-0.26511.14040.12161.1002-4.3573-0.07338.2055
62.6979-0.0732-0.42712.12970.72384.06770.1427-0.65540.15790.75060.1467-0.4254-0.4611.2543-0.27640.9267-0.2563-0.10560.6648-0.04370.57789.94188.747228.689
71.9881.0573-0.82972.91040.37813.00040.1525-0.1071-0.55310.2861-0.27310.3434-0.0887-0.1327-0.02890.5775-0.0952-0.10550.46410.01070.5259-4.0743-1.425223.5892
83.04290.2104-1.41972.3450.86443.64860.1043-0.12770.19620.2911-0.3742-0.607-0.37680.1893-0.19130.8784-0.1807-0.17520.58410.0430.63152.51584.796325.0207
93.33321.4829-3.05611.4714-1.07064.96640.29880.02190.7306-0.1954-0.3296-0.3577-1.0129-0.2262-0.16391.3406-0.0820.21620.7949-0.15571.5573-8.766220.884221.3656
101.4013-0.00610.24931.5370.06262.60360.24540.0650.1510.314-0.2501-0.0676-0.4264-0.1203-0.08960.5864-0.0419-0.02680.41760.00630.5346-7.23518.475910.7519
116.12283.1345-2.89685.03010.35265.34140.2877-0.20991.081-0.5721-0.06280.7879-1.9138-0.914-0.02240.62870.177-0.00980.5688-0.04760.7726-19.236717.16546.4967
123.4056-1.1125-0.07064.34311.67775.19020.05792.09541.068-1.17-0.02670.7746-0.6179-1.3029-0.0881.14890.1577-0.12550.96950.09380.8157-19.831316.9869-4.863
137.7862-0.31560.3792.52812.36657.77540.04190.7086-0.3503-0.6841-0.0024-0.0835-0.5788-0.1378-0.09960.52840.0508-0.06720.49390.00530.5591-9.07416.7662-5.9461
142.6030.2167-0.62462.92521.11553.33490.19140.0928-0.8234-0.1751-0.08090.02610.38330.1004-0.06930.611-0.0393-0.10050.46990.01140.7673-6.8186-10.97938.298
153.28920.42310.13043.3243-0.31565.42330.144-0.6169-0.14840.71290.26460.98820.0408-0.09940.01390.798-0.02420.09080.58270.00250.6453-17.1174.422416.7661
164.4778-0.7107-0.40076.11362.38065.3092-0.2208-0.6796-1.94741.5422-0.49491.31861.2786-0.63560.08260.9104-0.14830.12220.73050.14030.815-13.9607-8.502323.4974
174.97860.33681.00862.9337-0.6873.2229-0.0772-0.0885-1.0035-0.10320.17170.98810.2197-0.7327-0.3360.67190.08530.01511.06740.08330.8808-65.0712-20.4668-7.7221
185.0004-0.06270.67115.68951.39776.91180.12910.4899-1.1303-1.06110.05860.1437-0.5574-0.92-0.34680.77640.2663-0.12190.9724-0.23640.7264-54.5109-23.4229-11.9967
194.24890.6960.85392.7895-0.67311.458-0.0527-0.28960.15610.15980.10830.0365-0.2622-0.1534-0.12150.58090.11660.01040.8516-0.15680.5241-54.3155-7.5071-8.4706
206.18562.740.49366.3373-1.0125.97140.18822.2228-0.5334-0.244-0.5578-0.65280.9061.07-0.00080.86030.08890.07471.4824-0.1010.862-36.1144-10.755-17.1557
213.8469-0.36461.56681.7912-1.19822.55170.29691.0162-0.6313-0.1149-0.08880.3170.37760.0066-0.22740.57650.0905-0.01920.9521-0.23930.6521-51.1478-17.2198-10.2656
226.87290.49540.48473.32490.34842.983-0.13-0.0958-1.066-0.2805-0.1363-0.26610.9939-0.1165-0.17430.48820.02820.04150.6166-0.12260.7622-32.8741-22.72373.5941
234.2435-1.43092.04823.0394-0.08781.12520.22280.98490.557-0.8444-0.3532-0.12840.02670.00030.11880.55180.01950.05630.77910.03920.6512-35.7469-3.4819-9.3102
244.24671.05420.7613.3598-1.82812.8547-0.14910.4557-0.51050.3086-0.18670.12490.15410.1474-0.16740.46510.02660.00110.7752-0.14440.6474-41.2629-16.1389-3.4516
256.07431.1356-4.90021.8646-0.36768.6065-0.5917-0.04521.15250.8432-0.59640.9907-0.6142-0.97550.10040.62890.2323-0.24311.4076-0.2281.7293-45.67935.5717-0.1748
261.69150.66040.74123.54630.02740.7650.153-0.02770.17050.352-0.2790.2878-0.2428-0.57750.05310.58330.01680.08820.6925-0.09190.5858-39.9442-3.93417.6099
273.10240.6286-0.18422.24810.18772.21720.2928-0.39420.18761.0957-0.2950.3386-0.1775-0.23740.05970.7034-0.14890.06810.6639-0.06680.504-36.236-4.819116.165
285.84361.8262.31794.091.32533.17610.5959-1.90941.86991.2895-0.72080.2799-0.468-1.19960.23541.0476-0.07790.15250.9781-0.32380.7935-36.17767.574624.7717
292.9908-2.9241-2.66269.89741.64896.66660.4274-2.74730.45941.40060.01790.5969-0.4246-0.82580.17842.67010.12810.18742.2486-0.04351.174-42.3757-3.879733.5899
304.2085-0.09180.02143.3311.1213.2789-0.1209-0.7514-0.42031.01150.1452-0.2350.06470.2277-0.06050.9112-0.1526-0.1140.86660.05440.6518-26.5165-13.7120.6714
311.69541.26882.34564.2139-0.88485.23630.97290.4847-2.0721.13060.6960.04861.40550.6943-0.13580.8648-0.0343-0.21150.79350.0331.5181-24.1875-28.16912.7721
323.98360.51460.86784.0599-0.80252.56230.15340.4807-0.1710.0246-0.2738-0.6262-0.01010.20040.07120.3928-0.05070.02010.5294-0.00010.5876-23.3939-9.4474.5136
331.3663-1.00310.19521.35091.20244.48860.7214-0.18680.8076-0.59910.216-0.6399-1.12442.1159-0.89852.0779-0.79660.19491.4557-0.3711.166518.6726-29.006241.0286
340.4487-0.18380.25650.18510.3021.61690.84570.09561.0559-1.1336-0.6413-0.6721-2.31991.6363-0.72732.71-0.66070.40831.046-0.27411.15111.4617-19.700339.2726
351.6244-0.0686-0.26861.2913-0.55975.08840.1255-0.04160.48040.54950.2202-0.1123-1.8798-0.1212-0.40392.1933-0.46750.21280.9512-0.21610.84637.779-25.05839.9248
368.8156-2.18441.13697.7711.66072.17420.80520.00510.8023-0.2315-0.433-0.5492-0.8081-0.7777-0.02511.7797-00.10581.00990.0940.6206-4.653-33.391341.2645
370.4985-0.87580.29252.42-0.93780.41721.10280.00210.2764-0.4445-0.22370.0984-0.8415-1.79290.35942.25290.6183-0.38762.2632-0.22231.4876-15.5416-21.584740.2101
381.0403-1.0377-0.32532.46123.21067.76130.68590.11870.7309-1.8064-0.0547-0.629-2.272-0.2624-0.46092.3277-0.26130.17740.8268-0.07370.88473.5577-23.702641.241
394.8640.81671.77990.18980.27780.7851-0.54550.64371.6012-1.7453-0.0598-0.7579-2.97280.2809-0.28973.12080.01610.17651.0522-0.10021.20512.1533-8.204661.7147
401.4217-0.9721-0.53122.844-0.1260.26740.0069-0.20540.8081-1.5167-0.60770.4716-2.4762-2.27630.23582.6290.7005-0.25071.42-0.12231.1068-13.2226-13.169955.1384
412.8924-0.08150.1824.413.16079.85930.20660.87280.3185-0.2899-0.23450.5379-2.204-1.54760.27652.05190.3618-0.09161.0218-0.06860.6546-9.7829-27.108850.3298
422.4315-1.07440.29930.4616-0.16150.2175-0.08830.83630.4746-0.6636-0.2771-0.12580.1399-0.4793-0.03763.27780.11460.2621.31860.10381.1961-4.6911-7.731346.6479
433.34920.42650.70296.12341.49295.3289-0.0976-0.53060.3879-2.52480.7052-0.5797-1.897-0.8311-0.00611.7861-0.04930.05690.9149-0.15980.644-6.5394-27.592148.5618
449.9180.48852.07423.14141.9022.0645-0.1116-0.0864-0.5766-0.2027-0.43060.8130.2079-0.2656-0.13041.5653-0.05870.07111.0922-0.01011.9363-6.2283-41.447654.158
453.8603-1.1728-0.2072.72993.30599.25560.1701-0.1854-0.2166-0.4353-0.18660.12-1.0542-1.42550.08161.13620.03180.01030.937-0.06080.6097-7.9557-29.814567.6953
463.0053-0.09420.49235.40182.97199.5861-0.7123-1.6866-0.98441.08350.35260.37921.3834-1.69660.01971.3825-0.15680.06861.52420.08080.8488-8.8683-37.769484.878
470.887-0.90361.83862.5937-3.11853.6532-0.3112-0.3460.6775-0.6640.0036-0.2155-1.7816-1.65650.07032.00680.53550.01981.2804-0.21950.9906-10.2462-12.596574.852
481.8154-1.25740.68791.7778-1.42191.0958-0.30330.45970.23140.32720.47480.4619-1.7931-2.32710.311.7560.6158-0.15592.0256-0.27851.1132-20.6371-18.762562.5475
492.42130.0065-0.46013.9987-0.17825.46240.1703-0.1837-0.5677-0.3420.1481-0.55960.72130.3702-0.44940.6013-0.0906-0.19270.91340.08690.8458-54.313-38.59817.2974
504.13980.8291-1.6754.1097-0.92389.10520.43280.68930.2560.32930.1261-0.1786-0.0915-0.6804-0.43790.5456-0.1032-0.02730.86830.10140.5664-55.0272-27.52815.1855
511.8795-0.93030.8375.71610.01783.8415-0.02120.1045-0.02790.54110.29180.8162-0.3614-0.6932-0.47090.6021-0.0360.05620.97590.24910.6536-70.3903-31.275620.231
527.2567-3.21810.23284.58740.53049.1137-0.2057-0.03421.4536-1.3702-0.31210.3557-3.0636-1.0695-0.23011.43260.15650.12641.29160.30181.228-71.89-11.118715.0124
531.45390.240.57043.56730.73314.210.13850.22170.0509-0.32250.1137-0.3318-0.6614-0.1842-0.4110.6074-0.00810.04770.89260.1790.6946-61.5294-26.90415.9263
546.47560.22722.63035.5070.35852.13380.619-0.1096-0.86780.3563-0.4862-1.155-1.02481.4941-0.43110.9253-0.21370.09911.08860.08090.8451-50.9101-15.731536.4365
553.00830.62941.2373.53930.2874.9039-0.39230.22861.34480.1470.27161.0358-1.3776-0.4067-0.24251.08840.20310.20930.8180.29540.8405-67.4502-8.407928.3715
562.7247-0.04560.69862.9445-0.16024.21130.22880.3959-0.1510.33420.20950.2473-0.6698-0.4102-0.40310.70770.1030.15260.9010.17810.7073-64.367-18.130626.6345
572.813-3.82413.78468.9238-7.62896.73740.5352-0.3728-0.65940.42640.90681.40530.6599-1.6661-0.61971.0551-0.03090.22991.44190.11311.8264-80.7494-27.815630.7646
581.68720.51910.15543.4717-0.53024.43940.0032-0.5415-0.28810.46250.34970.7112-0.6209-0.9926-0.39770.80540.17940.25970.85440.23930.774-70.7608-19.699739.4042
591.4262-0.4709-0.57033.6606-0.28394.8305-0.4102-0.62050.20520.75840.64360.5735-0.2032-0.5389-0.41461.1610.21680.34460.85020.21440.6948-67.0439-19.752649.3337
601.655-0.00540.46824.15320.52172.67310.4277-0.68830.33281.28490.01260.8164-0.0329-2.157-0.30351.29880.28410.58951.70720.35721.2635-83.2868-21.614853.9961
615.22461.6372.11524.03910.82794.20131.2868-0.9788-0.8821.97540.0613-0.3116-1.316-1.5257-0.38361.54450.21140.29491.20920.23080.8198-69.3282-22.691761.8423
622.55290.31030.28734.6578-0.61385.003-0.0892-0.38690.52932.4150.52130.1807-1.33250.9621-0.37761.81930.16550.23680.87060.02590.9125-58.3709-1.995847.2934
632.79520.24560.68984.0702-0.49985.07050.0163-0.2910.45470.92650.33171.0848-1.8987-1.3444-0.32441.32620.42470.39491.0150.25570.9827-73.832-6.016539.5867
644.17841.75092.28996.82492.74498.7098-0.50330.00221.60490.4586-0.17420.9327-3.0167-0.6405-0.28271.83090.39980.29640.9660.26141.1026-69.68711.771133.049
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 134:139)A134 - 139
2X-RAY DIFFRACTION2(chain A and resid 140:164)A140 - 164
3X-RAY DIFFRACTION3(chain A and resid 165:184)A165 - 184
4X-RAY DIFFRACTION4(chain A and resid 185:213)A185 - 213
5X-RAY DIFFRACTION5(chain A and resid 214:219)A214 - 219
6X-RAY DIFFRACTION6(chain A and resid 220:252)A220 - 252
7X-RAY DIFFRACTION7(chain A and resid 253:284)A253 - 284
8X-RAY DIFFRACTION8(chain A and resid 285:313)A285 - 313
9X-RAY DIFFRACTION9(chain A and resid 314:321)A314 - 321
10X-RAY DIFFRACTION10(chain A and resid 322:379)A322 - 379
11X-RAY DIFFRACTION11(chain A and resid 380:395)A380 - 395
12X-RAY DIFFRACTION12(chain A and resid 396:410)A396 - 410
13X-RAY DIFFRACTION13(chain A and resid 411:421)A411 - 421
14X-RAY DIFFRACTION14(chain A and resid 422:458)A422 - 458
15X-RAY DIFFRACTION15(chain A and resid 459:470)A459 - 470
16X-RAY DIFFRACTION16(chain A and resid 471:482)A471 - 482
17X-RAY DIFFRACTION17(chain B and resid 134:166)B134 - 166
18X-RAY DIFFRACTION18(chain B and resid 167:185)B167 - 185
19X-RAY DIFFRACTION19(chain B and resid 186:210)B186 - 210
20X-RAY DIFFRACTION20(chain B and resid 211:219)B211 - 219
21X-RAY DIFFRACTION21(chain B and resid 220:246)B220 - 246
22X-RAY DIFFRACTION22(chain B and resid 247:271)B247 - 271
23X-RAY DIFFRACTION23(chain B and resid 272:284)B272 - 284
24X-RAY DIFFRACTION24(chain B and resid 285:313)B285 - 313
25X-RAY DIFFRACTION25(chain B and resid 314:320)B314 - 320
26X-RAY DIFFRACTION26(chain B and resid 321:351)B321 - 351
27X-RAY DIFFRACTION27(chain B and resid 352:391)B352 - 391
28X-RAY DIFFRACTION28(chain B and resid 392:407)B392 - 407
29X-RAY DIFFRACTION29(chain B and resid 408:414)B408 - 414
30X-RAY DIFFRACTION30(chain B and resid 415:432)B415 - 432
31X-RAY DIFFRACTION31(chain B and resid 433:443)B433 - 443
32X-RAY DIFFRACTION32(chain B and resid 444:481)B444 - 481
33X-RAY DIFFRACTION33(chain C and resid 135:157)C135 - 157
34X-RAY DIFFRACTION34(chain C and resid 158:167)C158 - 167
35X-RAY DIFFRACTION35(chain C and resid 168:197)C168 - 197
36X-RAY DIFFRACTION36(chain C and resid 198:212)C198 - 212
37X-RAY DIFFRACTION37(chain C and resid 213:220)C213 - 220
38X-RAY DIFFRACTION38(chain C and resid 221:247)C221 - 247
39X-RAY DIFFRACTION39(chain C and resid 248:255)C248 - 255
40X-RAY DIFFRACTION40(chain C and resid 256:273)C256 - 273
41X-RAY DIFFRACTION41(chain C and resid 274:294)C274 - 294
42X-RAY DIFFRACTION42(chain C and resid 295:301)C295 - 301
43X-RAY DIFFRACTION43(chain C and resid 302:314)C302 - 314
44X-RAY DIFFRACTION44(chain C and resid 315:320)C315 - 320
45X-RAY DIFFRACTION45(chain C and resid 321:395)C321 - 395
46X-RAY DIFFRACTION46(chain C and resid 396:412)C396 - 412
47X-RAY DIFFRACTION47(chain C and resid 413:443)C413 - 443
48X-RAY DIFFRACTION48(chain C and resid 444:481)C444 - 481
49X-RAY DIFFRACTION49(chain D and resid 135:166)D135 - 166
50X-RAY DIFFRACTION50(chain D and resid 167:188)D167 - 188
51X-RAY DIFFRACTION51(chain D and resid 189:211)D189 - 211
52X-RAY DIFFRACTION52(chain D and resid 212:219)D212 - 219
53X-RAY DIFFRACTION53(chain D and resid 220:243)D220 - 243
54X-RAY DIFFRACTION54(chain D and resid 244:255)D244 - 255
55X-RAY DIFFRACTION55(chain D and resid 256:281)D256 - 281
56X-RAY DIFFRACTION56(chain D and resid 282:313)D282 - 313
57X-RAY DIFFRACTION57(chain D and resid 314:320)D314 - 320
58X-RAY DIFFRACTION58(chain D and resid 321:357)D321 - 357
59X-RAY DIFFRACTION59(chain D and resid 358:378)D358 - 378
60X-RAY DIFFRACTION60(chain D and resid 379:404)D379 - 404
61X-RAY DIFFRACTION61(chain D and resid 405:419)D405 - 419
62X-RAY DIFFRACTION62(chain D and resid 420:447)D420 - 447
63X-RAY DIFFRACTION63(chain D and resid 448:473)D448 - 473
64X-RAY DIFFRACTION64(chain D and resid 474:481)D474 - 481

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万見について

-
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