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- PDB-4m10: Crystal Structure of Murine Cyclooxygenase-2 Complex with Isoxicam -

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基本情報

登録情報
データベース: PDB / ID: 4m10
タイトルCrystal Structure of Murine Cyclooxygenase-2 Complex with Isoxicam
要素Prostaglandin G/H synthase 2
キーワードOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / NSAID / COX / dioxygenase / peroxidase / glycosylation / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
機能・相同性
機能・相同性情報


Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / hair cycle / cellular response to homocysteine / Nicotinamide salvaging ...Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / hair cycle / cellular response to homocysteine / Nicotinamide salvaging / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / positive regulation of fibroblast growth factor production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / negative regulation of synaptic transmission, dopaminergic / cellular response to lead ion / response to nematode / positive regulation of transforming growth factor beta production / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of prostaglandin biosynthetic process / regulation of neuroinflammatory response / positive regulation of synaptic plasticity / positive regulation of smooth muscle contraction / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / response to fatty acid / response to fructose / positive regulation of fever generation / prostaglandin secretion / response to vitamin D / cellular response to fluid shear stress / nuclear outer membrane / response to angiotensin / response to manganese ion / prostaglandin biosynthetic process / nuclear inner membrane / negative regulation of smooth muscle contraction / cellular response to ATP / positive regulation of cell migration involved in sprouting angiogenesis / maintenance of blood-brain barrier / bone mineralization / negative regulation of calcium ion transport / decidualization / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / response to tumor necrosis factor / brown fat cell differentiation / response to glucocorticoid / keratinocyte differentiation / positive regulation of vasoconstriction / positive regulation of brown fat cell differentiation / embryo implantation / positive regulation of synaptic transmission, glutamatergic / learning / response to cytokine / caveola / positive regulation of smooth muscle cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / memory / regulation of blood pressure / positive regulation of protein import into nucleus / peroxidase activity / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / positive regulation of peptidyl-serine phosphorylation / response to estradiol / cellular response to heat / regulation of cell population proliferation / cellular response to hypoxia / angiogenesis / response to oxidative stress / response to lipopolysaccharide / response to xenobiotic stimulus / neuron projection / positive regulation of apoptotic process / negative regulation of cell population proliferation / heme binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / metal ion binding / cytoplasm
類似検索 - 分子機能
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily ...Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
PROTOPORPHYRIN IX CONTAINING FE / Chem-ICD / Prostaglandin G/H synthase 2
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.01 Å
データ登録者Xu, S. / Hermanson, D.J. / Banerjee, S. / Ghebreelasie, K. / Marnett, L.J.
引用ジャーナル: J.Biol.Chem. / 年: 2014
タイトル: Oxicams Bind in a Novel Mode to the Cyclooxygenase Active Site via a Two-water-mediated H-bonding Network.
著者: Xu, S. / Hermanson, D.J. / Banerjee, S. / Ghebreselasie, K. / Clayton, G.M. / Garavito, R.M. / Marnett, L.J.
履歴
登録2013年8月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年1月22日Provider: repository / タイプ: Initial release
改定 1.12014年2月12日Group: Database references
改定 1.22014年5月14日Group: Database references
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年9月20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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)277,77528
ポリマ－269,3314
非ポリマー8,44424
水31,3101738
1
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)138,88714
ポリマ－134,6652
非ポリマー4,22212
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-28 kcal/mol
Surface area42010 Å2
手法PISA
2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)138,88714
ポリマ－134,6652
非ポリマー4,22212
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-28 kcal/mol
Surface area41970 Å2
手法PISA
単位格子
Length a, b, c (Å)122.612, 134.077, 180.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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要素

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タンパク質 , 1種, 4分子 ABCD

#1: タンパク質
Prostaglandin G/H synthase 2 / Cyclooxygenase-2 / COX-2 / Glucocorticoid-regulated inflammatory cyclooxygenase / Gripghs / ...Cyclooxygenase-2 / COX-2 / Glucocorticoid-regulated inflammatory cyclooxygenase / Gripghs / Macrophage activation-associated marker protein P71/73 / PES-2 / PHS II / Prostaglandin H2 synthase 2 / PGH synthase 2 / PGHS-2 / Prostaglandin-endoperoxide synthase 2 / TIS10 protein


分子量: 67332.711 Da / 分子数: 4 / 断片: UNP residues 18-604 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 / プラスミド: pVL1393
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
株 (発現宿主): Sf21
参照: UniProt: Q05769, prostaglandin-endoperoxide synthase

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糖 , 3種, 16分子

#2: 多糖
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 4 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 8 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: 糖
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / オクチルβ-D-グルコピラノシド


タイプ: D-saccharide / 分子量: 292.369 Da / 分子数: 4 / 由来タイプ: 組換発現 / 式: C14H28O6 / コメント: 可溶化剤*YM
識別子タイププログラム
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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非ポリマー , 3種, 1746分子

#4: 化合物
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


分子量: 616.487 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C34H32FeN4O4
#5: 化合物
ChemComp-ICD / 4-hydroxy-2-methyl-N-(5-methyl-1,2-oxazol-3-yl)-2H-1,2-benzothiazine-3-carboxamide 1,1-dioxide / Isoxicam / イソキシカム


分子量: 335.335 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C14H13N3O5S / コメント: 抗炎症剤*YM
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1738 / 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: 2.75 Å3/Da / 溶媒含有率: 55.33 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8
詳細: mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM ...詳細: mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM DMSO stocks were added to protein samples. Mixing 3 uL of the protein-inhibitor complex with 3 uL crystallization solution containing 50 mM EPPS, pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550 against reservoir solutions comprised of 50 mM EPPS pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2012年11月19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: 0.9792 Å / 相対比: 1
反射解像度: 2→50.09 Å / Num. all: 197195 / Num. obs: 197072 / % possible obs: 99.77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 6.7 % / Biso Wilson estimate: 26.08 Å2 / Rsym value: 0.096 / Net I/σ(I): 25.96
反射 シェル解像度: 2→2.12 Å / 冗長度: 6.4 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.4 / Num. unique all: 28530 / Rsym value: 0.754 / % possible all: 99.7

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
PHASES位相決定
PHENIX(phenix.refine: 1.8.2_1309)精密化
XSCALEデータスケーリング
SCALAデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 3NT1, chain A

3nt1


解像度: 2.01→49.273 Å / SU ML: 0.19 / σ(F): 1.33 / 位相誤差: 27.58 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2201 9793 5 %RANDOM
Rwork0.1886 ---
obs0.1901 195768 99.11 %-
all-197195 --
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: 2.01→49.273 Å
タンパク質核酸リガンド溶媒全体
原子数17887 0 568 1738 20193
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01119051
X-RAY DIFFRACTIONf_angle_d1.22225852
X-RAY DIFFRACTIONf_dihedral_angle_d15.097000
X-RAY DIFFRACTIONf_chiral_restr0.0842737
X-RAY DIFFRACTIONf_plane_restr0.0063298
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.03220.29613210.27336079X-RAY DIFFRACTION98
2.0322-2.05610.2973170.25846087X-RAY DIFFRACTION99
2.0561-2.08110.28433230.25096134X-RAY DIFFRACTION98
2.0811-2.10750.29163190.24786043X-RAY DIFFRACTION98
2.1075-2.13520.2733220.23496156X-RAY DIFFRACTION99
2.1352-2.16450.28853260.23196112X-RAY DIFFRACTION99
2.1645-2.19540.28053210.22696106X-RAY DIFFRACTION99
2.1954-2.22820.26693210.23886093X-RAY DIFFRACTION98
2.2282-2.2630.28593230.24116088X-RAY DIFFRACTION98
2.263-2.30010.2783260.21886155X-RAY DIFFRACTION99
2.3001-2.33970.2663250.20326137X-RAY DIFFRACTION99
2.3397-2.38230.25013260.20126173X-RAY DIFFRACTION99
2.3823-2.42810.25623250.19246168X-RAY DIFFRACTION99
2.4281-2.47770.23933250.19066184X-RAY DIFFRACTION99
2.4777-2.53150.21873260.18766162X-RAY DIFFRACTION99
2.5315-2.59040.24833240.19156183X-RAY DIFFRACTION99
2.5904-2.65520.22783250.18416203X-RAY DIFFRACTION100
2.6552-2.7270.23723270.18876213X-RAY DIFFRACTION99
2.727-2.80720.22923240.1916206X-RAY DIFFRACTION100
2.8072-2.89780.25533260.19796202X-RAY DIFFRACTION99
2.8978-3.00140.22573300.19246242X-RAY DIFFRACTION100
3.0014-3.12150.22313300.19556258X-RAY DIFFRACTION100
3.1215-3.26360.21883280.19666220X-RAY DIFFRACTION99
3.2636-3.43560.22223280.18816229X-RAY DIFFRACTION99
3.4356-3.65080.1863310.17256280X-RAY DIFFRACTION100
3.6508-3.93250.18043320.16236306X-RAY DIFFRACTION100
3.9325-4.32810.17473320.15336320X-RAY DIFFRACTION100
4.3281-4.95390.17083320.15066302X-RAY DIFFRACTION99
4.9539-6.23940.17943350.16756403X-RAY DIFFRACTION100
6.2394-49.28810.2033430.18156531X-RAY DIFFRACTION98
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)
19.25190.10781.46011.69611.17772.58930.29730.26830.52730.0747-0.06430.0985-0.3625-0.2758-0.21570.5260.10030.10370.18040.04840.2617116.356261.574836.7025
25.05950.9787-3.40843.9437-0.72482.2940.48040.39390.8101-0.6883-0.12810.1526-0.374-0.1735-0.24890.6050.20340.07750.31220.06130.4547110.245565.104742.4978
31.28241.8736-1.55323.1642-3.1954.17690.36890.00280.5178-0.3588-0.1793-0.3663-0.7623-0.071-0.20220.59770.00390.1530.16530.02030.4299125.805569.320641.348
40.8622-1.9176-1.80174.27343.99513.74760.5662-0.12920.9108-1.03110.526-1.267-0.9886-0.0297-0.98360.6266-0.12940.29820.3756-0.00840.7233139.176464.663132.878
52.5219-1.0669-0.19552.2997-1.52893.30390.36680.07990.29480.0999-0.2995-0.10090.07020.7165-0.04490.2949-0.17220.08850.4151-0.01790.4382153.49349.548732.0569
69.05-2.52040.85240.81390.0370.6998-0.1387-0.20991.89170.04770.2397-0.1149-0.71630.38260.01680.5382-0.13170.07230.2887-0.05370.4777139.952852.970839.7286
71.06740.16-0.23570.867-0.22372.48470.17110.02890.1895-0.0339-0.1141-0.0167-0.3418-0.2304-0.08510.22050.06130.00890.14320.00070.1639118.583647.305845.0457
81.5408-2.0022-1.45154.24513.23642.7680.21730.49880.0524-0.1702-0.54990.3777-0.317-0.71850.2650.36360.1937-0.02010.46420.01320.3138112.041548.173821.9766
95.95350.0471-0.63422.3869-0.04910.57540.22540.57060.024-0.4963-0.1851-0.0875-0.3281-0.0303-0.07580.32830.10970.06090.34860.02630.184134.192336.229713.9932
101.6747-1.35480.30661.40150.35531.1799-0.0320.0708-0.24-0.0248-0.00990.1718-0.0236-0.13620.04270.17730.003-0.00360.1832-0.01240.2035127.993230.623438.7275
111.85630.0995-0.17382.59490.87973.16070.03530.0713-0.44030.0332-0.0964-0.01810.39850.16260.05250.24790.040.01890.13060.01480.3061134.797612.942744.5459
123.92651.72962.09426.7741-2.0495.89120.10840.1211-0.699-0.19330.05320.51420.4526-0.36640.01710.2024-0.0082-0.0180.2109-0.09220.4096122.265113.366937.5836
137.03171.97433.13885.21892.98317.58090.28810.4941-0.5079-0.275-0.3670.38020.9493-0.19140.16790.36010.0221-0.0050.2397-0.02470.2813126.228615.258635.3565
140.889-0.1291-0.06861.0799-0.19792.56370.0262-0.0319-0.09480.0533-0.0471-0.09980.17410.30940.0240.13540.0360.02120.1927-0.00760.1919142.173824.656243.7979
151.73560.8867-2.50381.9259-1.42028.59820.2011-0.31630.1857-0.16810.0771-0.1504-0.04081.2801-0.22620.19430.00360.06690.3161-0.0220.2812148.115844.14638.1687
161.4716-0.8049-0.70080.43170.69073.14250.05050.06270.1561-0.1027-0.0585-0.1744-0.1534-0.0167-0.01050.2050.01790.02470.14070.02550.2182131.77242.457738.5913
173.1380.50311.51864.0945-0.93781.97560.17360.5134-0.3279-0.5535-0.1201-0.01720.22330.1145-0.05960.26240.0869-0.00880.273-0.08630.2581135.147418.503421.3382
181.1535-0.0858-0.12680.82940.07681.58580.15490.34860.1836-0.2986-0.0732-0.0043-0.3848-0.2393-0.07260.37280.12850.02490.30270.060.2134123.088947.773521.5782
191.341-0.2903-0.19070.3880.5641.37960.0564-0.02790.0701-0.03870.0328-0.1388-0.07720.286-0.05890.1489-0.01760.02910.2061-0.01660.2009143.318735.578639.3565
203.304-0.1402-4.64172.53710.61299.63880.02330.11310.1007-0.3092-0.3089-0.0596-0.05631.80430.22010.20360.0627-0.01170.33140.05390.1829146.412431.410123.3939
211.8081-0.513-0.34762.22850.5293.17370.0475-0.4347-0.01870.08470.0485-0.09230.41060.3301-0.11030.30240.1043-0.01740.6152-0.00740.2724149.441728.436468.0519
222.082.36060.23062.68470.1743.068-0.1303-0.2621-0.08260.14160.13-0.58740.26860.9057-0.02350.20190.0389-0.03490.7735-0.12810.3409154.989934.595365.6088
233.9208-3.40570.89133.51590.66483.9361-0.1419-0.70531.60620.4607-0.037-1.1764-0.78030.94990.220.515-0.2434-0.04280.9144-0.22640.7109158.157949.630768.838
243.5710.24912.77976.589-0.95982.37060.5284-0.9290.3679-0.55760.2412-1.12110.17330.2393-0.48440.3057-0.09330.02140.5052-0.1520.7655144.024656.639479.7785
252.1773-0.94543.11813.0195-0.26537.9344-0.4172-0.01420.1133-0.02330.1838-0.2831-1.42770.36330.19840.4633-0.15390.02740.3454-0.14130.473134.772469.380175.3783
260.1062-0.91040.35977.5515-2.27591.8496-0.1445-0.22530.1486-0.3097-0.1495-1.45160.09520.94720.080.3196-0.19780.05030.5267-0.13780.4322138.454357.654866.9495
273.12370.34871.13911.00880.65513.8509-0.1086-0.3188-0.03570.05760.1025-0.10770.16790.43430.01310.15880.03890.01710.2194-0.00790.1472135.253731.334663.6573
285.9888-2.7182-2.85832.9251.5372.3164-0.1268-0.2513-0.30480.4606-0.07440.07850.6260.31510.14530.37840.1528-0.03350.52410.04570.1801132.690529.249689.0552
291.2494-0.8385-0.32811.14550.99591.8573-0.0586-0.26960.03010.15810.058-0.0699-0.05560.1208-0.02380.1785-0.00140.00050.262-0.02970.1589119.238147.656979.1308
306.303-3.85331.92923.9267-3.53087.495-0.1686-0.2755-0.62590.14680.1181.19010.1742-0.50330.00650.27350.02180.06060.21610.03270.25120.662528.989367.2786
313.545-0.7504-1.35760.83670.38822.39060.09380.0336-0.0902-0.0863-0.12410.1276-0.0075-0.28640.02980.1760.0053-0.00220.1908-0.02710.1834104.787345.3962.5597
326.36230.42680.84077.458-4.74976.9741-0.1243-0.0087-0.74190.01760.6080.45910.0187-0.7376-0.40130.15670.01120.01240.26070.07190.3358101.180334.908670.2589
331.3237-0.00120.01890.52560.10561.59420.0214-0.14870.1509-0.01060.00140.0101-0.2832-0.09520.00350.20070.03190.0140.1609-0.04240.1971112.379253.553766.0553
340.8163-0.672-0.27740.86240.58481.6707-0.05-0.2680.05520.08460.0243-0.1356-0.09910.22330.00970.1572-0.0218-0.02440.2695-0.0490.1951128.102946.126970.1986
352.12411.64910.00636.48980.47832.0775-0.0237-0.72540.14151.01830.25570.63730.1789-0.4608-0.2870.43510.09680.03690.50730.04860.3118105.502145.633290.1123
365.1270.53781.97541.7653-1.22032.1719-0.1755-0.57150.02470.10560.25720.055-0.1167-0.3878-0.06070.26670.05430.04030.4035-0.06620.2274104.878550.481283.5413
370.6696-0.32-0.29620.55720.4561.7072-0.0174-0.3350.00860.18760.124-0.09980.04810.3572-0.0970.21870.0521-0.04490.4132-0.02290.1967133.868537.169183.3225
380.519-1.3943-0.38487.1883-1.51683.8744-0.2161-0.48440.05010.97510.4559-0.4770.0260.1892-0.20130.3310.1271-0.07580.8217-0.02890.2939137.927936.837996.8067
390.8025-0.3096-0.05840.7835-0.221.2765-0.0186-0.25170.19390.1080.0487-0.1119-0.19920.1453-0.02710.2147-0.03390.01480.2332-0.08830.2132125.366651.952572.1259
408.4132-2.03531.98769.2162-5.99164.59890.2317-0.5211.3520.97920.5138-0.3704-1.97121.0101-0.71040.3937-0.02630.03860.4449-0.14330.3818118.540659.701983.9227
411.8065-0.99851.09558.3217-1.05612.65780.01290.19110.1711-0.3458-0.0347-0.3309-0.37360.3610.03630.2483-0.08220.03810.4296-0.00470.22487.361936.940525.3909
424.9042-3.7371-0.13347.68194.29853.8014-0.07390.23210.0675-0.45640.2195-0.7658-0.34840.3961-0.09790.2688-0.15060.04620.4165-0.00620.25790.903743.017631.2082
435.5041-0.1573-2.5371.41651.32434.54310.0470.2816-0.217-0.30030.1845-0.29310.20310.9144-0.22190.18640.02420.02790.4806-0.05860.25394.459228.295330.1416
449.38360.98553.3225.14182.0576.88170.35171.1886-0.6940.05580.0184-1.03941.14880.5609-0.37110.48850.20630.02950.589-0.09910.693695.13615.170125.3831
453.8186-1.08240.66724.83432.22291.41750.71630.7336-0.9175-0.2481-0.0689-1.0840.22760.7427-0.6210.31220.08910.0310.419-0.10430.680682.743412.47615.8289
462.670.526-2.32292.49410.2865.1812-0.25860.1394-0.0989-0.03780.0639-0.17370.6553-0.18040.20990.25160.08090.04220.2442-0.03360.379174.50270.094120.6475
473.81493.39872.21863.43121.28784.53370.0878-0.533-0.20160.25870.4305-1.40990.18460.6902-0.34180.39570.0388-0.04560.49560.00250.516978.124512.577928.41
482.14450.7753-0.10261.2912-0.52653.0372-0.05060.0984-0.06590.05730.0199-0.1223-0.08440.27250.03670.129-0.028-0.00590.12350.00430.121973.109734.658433.4998
496.18253.39473.66892.01761.62943.217-0.52130.58270.5763-0.31790.14530.0252-0.54770.47660.42060.3517-0.116-0.01970.35520.07140.296478.389644.532714.7577
500.96880.7021-0.07231.3596-0.13611.534-0.09670.16850.0675-0.13990.04330.0843-0.07090.01820.05110.13930.0049-0.02650.21260.01370.16559.888224.72812.7657
513.73543.2764-0.93537.6033-2.46575.72210.06580.0180.52650.3877-0.07210.4892-0.4399-0.35740.03610.12860.01160.01050.19010.01040.204760.11233.719731.2592
523.87420.09081.27811.0040.61773.1686-0.0967-0.00080.1655-0.0383-0.06320.0932-0.0941-0.32530.15580.15260.0140.01850.1566-0.02280.197841.112521.787733.3976
532.3946-1.61893.62684.7289-2.98995.9862-0.1471-0.03140.5217-0.14150.04680.1104-0.3927-0.37210.03760.21910.0306-0.03460.21420.00820.260339.539330.377723.0594
540.9991-0.0599-0.44560.51040.07812.2080.00510.0456-0.0880.0304-0.00070.06860.1868-0.12780.03920.1492-0.0306-0.00380.1202-0.04120.176551.355712.342130.7006
551.44940.19211.13930.7691-0.33652.5138-0.00140.2544-0.074-0.15160.02630.0220.12690.0035-0.03720.12910.01260.04440.2021-0.02580.153560.756719.075521.1041
566.5983-1.6613-2.22552.6184-1.4243.1667-0.09930.2882-0.0891-0.1130.15530.27420.1013-0.4118-0.07290.2034-0.0591-0.05480.2578-0.03180.211643.500616.73812.3599
570.98710.11260.80480.48490.12151.4525-0.02110.2340.0533-0.06670.0151-0.0387-0.05810.25130.00770.1739-0.03260.02110.27260.03560.146472.391830.336612.672
581.6756-0.1475-0.07793.0565-0.39175.7346-0.0620.52670.2423-0.30580.0172-0.1972-0.25970.24610.04590.2125-0.07220.00790.370.03460.158476.612832.96355.2764
590.42620.30730.23221.0251-0.17930.4126-0.03520.0886-0.119-0.02990.0142-0.06370.15490.00810.05510.1926-0.00130.00990.1698-0.04660.187761.749711.634226.5855
606.31142.0887-0.66434.4202-2.02632.9471-0.1824-0.0667-0.0066-0.4078-0.1156-0.01620.97170.15850.26290.2465-0.03240.02610.2182-0.05380.233656.11438.251913.3808
613.1134-0.93321.89731.0340.42252.40750.0496-0.284-0.21260.2186-0.06140.06490.3382-0.30560.02760.3886-0.09240.00910.20990.02060.257653.35894.578756.5277
624.7235-3.05290.48613.6646-0.764.55490.0786-0.109-0.80.3329-0.0863-0.29150.76620.10820.02820.47140.0089-0.09080.14120.03220.328764.791-2.314555.0825
633.0557-0.6215-0.56056.50610.22674.71390.47240.0974-0.54240.5147-0.2350.17960.67840.3823-0.24760.25690.0835-0.06660.26780.0370.463985.098511.379469.0529
645.4431-1.39350.1244.8209-1.72125.17980.16220.4235-0.3468-0.3713-0.2127-0.249-0.02081.29770.00940.20690.12040.01920.47440.04880.350594.447518.810858.8999
656.7513.7673-2.50723.3324-0.01284.28740.05680.3698-1.3610.00780.1835-0.68261.16120.094-0.16840.55350.1402-0.02950.3128-0.09890.445779.783514.222955.8722
660.6572-0.43670.24511.8059-0.57873.5160.0082-0.0498-0.06290.0002-0.06650.08470.2415-0.28160.02930.1685-0.0461-0.00080.1195-0.01230.174655.981918.225353.442
672.46252.42750.6667.28642.48312.8351-0.0938-0.34850.11150.1166-0.14350.44080.2263-0.39790.13280.2831-0.12340.04130.27570.01910.146855.0122.575579.0967
680.8320.52280.57291.0194-0.0221.47160.0782-0.11990.05340.0115-0.1142-0.08630.05840.1290.02020.1315-0.0111-0.00690.1379-0.00360.175873.107834.397567.7324
695.31751.511-3.97543.5-0.41686.04040.20890.02790.77140.1358-0.00880.3948-0.3224-0.3507-0.15420.1476-0.01450.0010.1347-0.02920.24558.206932.907854.1477
701.68490.24630.49462.72690.72893.4674-0.02260.01210.1782-0.07-0.03550.054-0.299-0.0840.05360.1567-0.0063-0.01810.10690.02150.21572.193550.488151.0335
715.4964-0.0151-4.1485.6147-1.77287.63460.046-0.09480.2969-0.1096-0.0520.2982-0.3836-0.3371-0.0580.13790.009-0.01540.1601-0.01920.35361.044553.739558.5827
725.0651-2.5363-3.46715.60033.96458.43790.1581-0.220.29440.02450.0006-0.0022-0.6931-0.1973-0.09480.1998-0.0001-0.0190.15780.00940.172565.020751.514861.0811
730.4337-0.1494-0.09270.676-0.14931.4380.0201-0.00320.00720.0124-0.0301-0.0895-0.05380.27250.02420.1179-0.0242-0.02040.1698-0.00650.186182.081938.33953.1641
740.70190.35740.23761.61271.27882.18140.0734-0.10910.01920.1359-0.0776-0.06180.08150.03750.01670.18330.0095-0.01490.14220.02490.188670.701928.929362.4834
754.6329-0.9618-1.20323.9905-1.24912.19720.1669-0.39290.23430.3409-0.06810.1361-0.220.0175-0.09050.2449-0.0520.01870.2579-0.04180.200173.896349.372673.8778
761.59510.81740.73630.92210.78010.94760.1086-0.08130.04970.1402-0.07390.07750.158-0.241-0.03430.243-0.06040.01810.25010.01060.179562.63929.622875.2131
771.26790.17050.57491.75330.10993.48680.1748-0.2277-0.24960.155-0.0346-0.01690.70480.0428-0.18450.2778-0.05120.00060.14990.03280.175363.915312.401970.9502
783.8691-0.18083.05175.1826-4.09045.4073-0.0745-0.77920.07380.4283-0.33080.0510.2399-0.19920.42010.3854-0.13050.03910.34530.03760.238959.072316.529384.5117
791.85230.0835-0.391.57270.04682.65910.0693-0.22-0.23770.3237-0.0791-0.05390.1879-0.07030.01080.2465-0.0318-0.02010.1150.03360.16167.755518.282671.6901
800.76160.61740.13571.11310.98812.4943-0.0192-0.0280.01930.0530.0816-0.05790.04550.3979-0.08860.12050.0191-0.02240.21670.00240.214185.225536.013353.8491
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 33:45)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 46:56)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 57:74)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 75:89)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 90:114)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 115:123)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 124:156)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 157:183)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 184:193)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 194:239)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 240:266)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 267:278)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 279:292)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 293:352)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 353:366)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 367:391)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 392:429)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 430:511)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 512:578)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 579:583)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 33:52)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 53:70)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 71:81)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 82:92)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 93:110)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 111:122)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 123:160)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 161:186)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 187:212)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 213:222)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 223:267)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 268:278)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 279:364)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 365:394)
35X-RAY DIFFRACTION35(CHAIN B AND RESID 395:407)
36X-RAY DIFFRACTION36(CHAIN B AND RESID 408:430)
37X-RAY DIFFRACTION37(CHAIN B AND RESID 431:482)
38X-RAY DIFFRACTION38(CHAIN B AND RESID 483:493)
39X-RAY DIFFRACTION39(CHAIN B AND RESID 494:578)
40X-RAY DIFFRACTION40(CHAIN B AND RESID 579:583)
41X-RAY DIFFRACTION41(CHAIN C AND RESID 33:45)
42X-RAY DIFFRACTION42(CHAIN C AND RESID 46:56)
43X-RAY DIFFRACTION43(CHAIN C AND RESID 57:73)
44X-RAY DIFFRACTION44(CHAIN C AND RESID 74:83)
45X-RAY DIFFRACTION45(CHAIN C AND RESID 84:89)
46X-RAY DIFFRACTION46(CHAIN C AND RESID 90:114)
47X-RAY DIFFRACTION47(CHAIN C AND RESID 115:122)
48X-RAY DIFFRACTION48(CHAIN C AND RESID 123:156)
49X-RAY DIFFRACTION49(CHAIN C AND RESID 157:174)
50X-RAY DIFFRACTION50(CHAIN C AND RESID 175:214)
51X-RAY DIFFRACTION51(CHAIN C AND RESID 215:228)
52X-RAY DIFFRACTION52(CHAIN C AND RESID 229:271)
53X-RAY DIFFRACTION53(CHAIN C AND RESID 272:289)
54X-RAY DIFFRACTION54(CHAIN C AND RESID 290:357)
55X-RAY DIFFRACTION55(CHAIN C AND RESID 358:407)
56X-RAY DIFFRACTION56(CHAIN C AND RESID 408:430)
57X-RAY DIFFRACTION57(CHAIN C AND RESID 431:482)
58X-RAY DIFFRACTION58(CHAIN C AND RESID 483:506)
59X-RAY DIFFRACTION59(CHAIN C AND RESID 507:577)
60X-RAY DIFFRACTION60(CHAIN C AND RESID 578:582)
61X-RAY DIFFRACTION61(CHAIN D AND RESID 33:52)
62X-RAY DIFFRACTION62(CHAIN D AND RESID 53:80)
63X-RAY DIFFRACTION63(CHAIN D AND RESID 81:99)
64X-RAY DIFFRACTION64(CHAIN D AND RESID 100:114)
65X-RAY DIFFRACTION65(CHAIN D AND RESID 115:122)
66X-RAY DIFFRACTION66(CHAIN D AND RESID 123:164)
67X-RAY DIFFRACTION67(CHAIN D AND RESID 165:186)
68X-RAY DIFFRACTION68(CHAIN D AND RESID 187:212)
69X-RAY DIFFRACTION69(CHAIN D AND RESID 213:228)
70X-RAY DIFFRACTION70(CHAIN D AND RESID 229:265)
71X-RAY DIFFRACTION71(CHAIN D AND RESID 266:278)
72X-RAY DIFFRACTION72(CHAIN D AND RESID 279:293)
73X-RAY DIFFRACTION73(CHAIN D AND RESID 294:367)
74X-RAY DIFFRACTION74(CHAIN D AND RESID 368:398)
75X-RAY DIFFRACTION75(CHAIN D AND RESID 399:428)
76X-RAY DIFFRACTION76(CHAIN D AND RESID 429:457)
77X-RAY DIFFRACTION77(CHAIN D AND RESID 458:485)
78X-RAY DIFFRACTION78(CHAIN D AND RESID 486:494)
79X-RAY DIFFRACTION79(CHAIN D AND RESID 495:530)
80X-RAY DIFFRACTION80(CHAIN D AND RESID 531:583)

+
万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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