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- PDB-6v3r: Crystal structure of murine cycloxygenase in complex with a harma... -

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基本情報

登録情報
データベース: PDB / ID: 6v3r
タイトルCrystal structure of murine cycloxygenase in complex with a harmaline analog, 4,9-dihydro-3H-pyrido[3,4-b]indole
要素Prostaglandin G/H synthase 2
キーワードOXIDOREDUCTASE/INHIBITOR / Prostaglandin G/H synthase 2 / CYCLOOXYGENASE-2 / OXIDOREDUCTASE / INHIBITOR COMPLEX / MEMBRANE PROTEIN / 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 / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity ...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 / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / 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 fever generation / response to selenium ion / cellular response to fluid shear stress / prostaglandin secretion / response to nematode / nuclear inner membrane / prostaglandin biosynthetic process / dioxygenase activity / bone mineralization / nuclear outer membrane / decidualization / brown fat cell differentiation / keratinocyte differentiation / positive regulation of brown fat cell differentiation / embryo implantation / peroxidase activity / regulation of blood pressure / regulation of cell population proliferation / response to oxidative stress / cellular response to hypoxia / neuron projection / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / metal ion binding / cytosol / 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 ...: / 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-Y8A / 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: 2.66 Å
データ登録者Xu, S. / Uddin, M.J. / Banerjee, S. / Marnett, L.J.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI)CA89450 米国
引用ジャーナル: Acs Med.Chem.Lett. / 年: 2020
タイトル: Harmaline Analogs as Substrate-Selective Cyclooxygenase-2 Inhibitors.
著者: Uddin, M.J. / Xu, S. / Crews, B.C. / Aleem, A.M. / Ghebreselasie, K. / Banerjee, S. / Marnett, L.J.
履歴
登録2019年11月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年2月26日Provider: repository / タイプ: Initial release
改定 2.02020年7月29日Group: Atomic model / Data collection ...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 / 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.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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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 2.12020年11月4日Group: Database references / Structure summary / カテゴリ: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
改定 2.22023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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)277,20426
ポリマ－269,3314
非ポリマー7,87322
水4,396244
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)138,60213
ポリマ－134,6652
非ポリマー3,93711
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-27 kcal/mol
Surface area42230 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)138,60213
ポリマ－134,6652
非ポリマー3,93711
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10500 Å2
ΔGint-26 kcal/mol
Surface area42170 Å2
手法PISA
単位格子
Length a, b, c (Å)217.154, 124.379, 136.539
Angle α, β, γ (deg.)90.000, 123.838, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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 / PGHS-2 / Prostaglandin-endoperoxide synthase 2 / TIS10 protein


分子量: 67332.711 Da / 分子数: 4 / 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 / 細胞株 (発現宿主): Sf21
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q05769, prostaglandin-endoperoxide synthase

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糖 , 3種, 14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: 天然
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
#4: 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


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 8 / 由来タイプ: 天然 / 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
#5: 糖 ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


タイプ: D-saccharide / 分子量: 292.369 Da / 分子数: 2 / 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, 252分子

#3: 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
#6: 化合物
ChemComp-Y8A / 9-[(4-chlorophenyl)methyl]-6-methoxy-1-methyl-4,9-dihydro-3H-beta-carboline


分子量: 338.831 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C20H19ClN2O / タイプ: SUBJECT OF INVESTIGATION
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 244 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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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: 3.01 Å3/Da / 溶媒含有率: 59.2 %
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: 6.7
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
PH範囲: 6.4-7.0

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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: APS / ビームライン: 24-ID-E / 波長: 0.97918 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2016年4月13日
放射モノクロメーター: Cryogenically-cooled single crystal
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: 0.97918 Å / 相対比: 1
反射解像度: 2.66→102.39 Å / Num. obs: 85034 / % possible obs: 97.95 % / 冗長度: 3.1 % / Biso Wilson estimate: 42.64 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.1573 / Rpim(I) all: 0.1063 / Rrim(I) all: 0.1905 / Net I/σ(I): 8.39
反射 シェル解像度: 2.66→2.757 Å / 冗長度: 3 % / Rmerge(I) obs: 1.076 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 7373 / CC1/2: 0.521 / Rpim(I) all: 0.738 / % possible all: 85.82

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3NT1

3nt1


解像度: 2.66→102.39 Å / SU ML: 0.4229 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 31.0923
Rfactor反射数%反射
Rfree0.2638 2536 3 %
Rwork0.2194 --
obs0.2207 84666 97.96 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 49.35 Å2
精密化ステップサイクル: LAST / 解像度: 2.66→102.39 Å
タンパク質核酸リガンド溶媒全体
原子数17896 0 532 247 18675
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002119104
X-RAY DIFFRACTIONf_angle_d0.550926010
X-RAY DIFFRACTIONf_chiral_restr0.04062746
X-RAY DIFFRACTIONf_plane_restr0.00373336
X-RAY DIFFRACTIONf_dihedral_angle_d19.74677066
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.710.38021000.32283507X-RAY DIFFRACTION75.4
2.71-2.770.34891430.30544556X-RAY DIFFRACTION98.95
2.77-2.830.33761520.30394607X-RAY DIFFRACTION99.33
2.83-2.890.331370.31094620X-RAY DIFFRACTION99.17
2.89-2.970.40871480.3114636X-RAY DIFFRACTION99.36
2.97-3.050.34671430.29494596X-RAY DIFFRACTION99.68
3.05-3.140.35211380.27534618X-RAY DIFFRACTION99.85
3.14-3.240.30741470.25814635X-RAY DIFFRACTION99.87
3.24-3.350.28891380.25294657X-RAY DIFFRACTION99.92
3.35-3.490.2821440.23484658X-RAY DIFFRACTION99.88
3.49-3.650.28731420.2534505X-RAY DIFFRACTION97.85
3.65-3.840.33141400.25814569X-RAY DIFFRACTION98.04
3.84-4.080.21231480.17924643X-RAY DIFFRACTION99.73
4.08-4.390.20471420.16044655X-RAY DIFFRACTION99.77
4.39-4.840.20751430.14894649X-RAY DIFFRACTION99.58
4.84-5.540.20441410.15144659X-RAY DIFFRACTION99.32
5.54-6.970.2071430.19724672X-RAY DIFFRACTION99.22
6.97-102.390.21271470.18214688X-RAY DIFFRACTION98.23
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)
1-0.0281298289271-0.3889814430730.4448665458312.38668250476-1.777156190625.82775117048-0.203609726127-0.1350450637910.4828972918270.390714913096-0.0656740946506-0.0129343050445-1.178025595160.3135974769350.3005985852180.596772456721-0.0395955466617-0.2973194181740.429096547294-0.06700572955470.686090019561-41.2471080156-6.9156897928719.6204530065
25.514827693951.094567210310.5435033204174.801863412090.7805200067487.65307523677-0.24866578809-0.3188449304580.746713774084-0.02698406686680.2504304618050.0377536228123-0.663554689522-0.581367734302-0.02513599958630.3936127790280.0525077797717-0.04459603849960.315123329427-0.1307028569250.479988464449-55.0734074996-22.024031152139.1104715329
32.37183903945-0.6753411399782.950333147431.38337531679-0.6410719936235.1405468613-0.06506602956140.09165890352910.379208002150.237041403482-0.160717425025-0.540306024775-0.1403937094330.3314962429990.192651404990.352261748605-0.024141020937-0.09236350232180.235620408710.008110002371470.425952404485-32.9840397-22.990856527511.9214593345
41.18218971759-0.213396560562-0.5208430360641.84881722473-0.994704587892.219189336470.09074882201560.0406436969224-0.0714749703452-0.02387619514730.1725709981120.01248811324830.468509866305-0.094624088802-0.2801593726750.4106789218070.0164255710914-0.2217636509640.267494151499-0.03401577259820.529019282359-37.2550605974-38.214058613124.7881652431
52.15754557727-1.55107590261-1.002083118813.73563326197-0.9283291332771.47346986684-0.09956574009060.009160172283440.04000747238840.01106804821930.018833111283-0.2580054225980.07913945418450.02332543674050.04152372048670.398416397622-0.0357105736201-0.1839244110920.324550896748-0.005880310947080.377495643931-45.521575338-56.018211489918.3857801573
61.11491888498-0.3810195711340.1911570243321.64805467366-0.6432443134811.2351760860.0960394993746-0.19102258401-0.2037796577270.1666805831020.0755691750491-0.004032665819810.196278777247-0.032083810791-0.1698992714610.339800918462-0.0224727560526-0.1423954271810.322778713961-0.01174932064390.342884436701-53.5342280566-39.564845321626.9283146165
76.319098411232.21630445231-2.001586603643.96060731475-0.5664995865310.8456155186850.364816270451-0.500967137192-0.9909007050610.667627156493-0.333946288335-0.8443429121280.1383301922230.418995703209-0.0137246159070.6264407548790.0115732687014-0.3252427844290.4319325054310.06569222932230.679690780911-33.4791669995-53.213890664135.3124929401
81.10237144331-1.007082981410.3154447427041.07176385443-0.7289956610511.07494646189-0.110641989145-0.09079535365340.25110937970.2680486700470.0712846527533-0.266977482659-0.1197611658640.2201836255930.04956212163860.401942516445-0.0146704291093-0.1956583754520.399377933412-0.04937529685510.487093095474-30.0596753649-24.260654265927.8707704862
93.994570682620.6656983167870.6631083610833.392074958150.7367941377171.7438715522-0.190064089797-0.6610779047220.2418137426930.6379096924060.116510810662-0.331657002317-0.178711078873-0.4787130693670.08071096707350.363656023963-0.00463642104226-0.09246646380930.386423490772-0.04972186772440.288812406507-57.2586395063-42.112979017632.4456817602
101.04526706279-0.4278838138930.09326341973484.68115907719-3.426523106953.41688507996-0.0140697327728-0.2628683200750.1046081585030.254091028820.4758881404990.713141338606-0.343262396562-0.742854636518-0.4631069875280.3859183330250.0950052347023-0.05466516324390.677750502118-0.06821190121880.497282242072-81.1264985099-26.385416018715.0550154871
111.044081274120.5028666979760.409894827486.48925246761-3.290674603451.80331262146-0.00573832471205-0.2839229661050.2046292941880.6764558916820.3259738919970.39604001887-0.322164659298-0.371127544796-0.3024449681070.3679138901620.0680475842258-0.02308630994910.504503232898-0.05295062458930.409478843891-68.9179432222-23.667266803810.2591765348
120.7980920049260.140148222140.1862768680.78999837801-0.3847427391821.338489587590.08870211984190.0247946977938-0.246438526982-0.0758731791898-0.01309231117940.06659271189730.141732293179-0.134984614857-0.07227155646740.3734689404620.0128404688962-0.1195215441230.27357136646-0.006880440661960.376803948706-63.1476051198-32.3490086827-8.47596793744
135.890428422823.903305983493.369809102922.191313504982.994335790714.47425789679-0.3066847190890.703561607004-0.127025604421-0.7635843138030.399921834464-0.268913065436-0.1726524096690.172975629862-0.2659631835470.3817952653870.0131849807799-0.04104935535560.3858786002240.06495839762910.355928332598-51.4916450242-23.8986817777-17.8594904731
141.107228704180.2675993601760.09021352767630.911887983721-0.09736552750150.548916646117-0.02460262666230.1052451207550.0695280909123-0.162931214319-0.01666504952060.142196227736-0.00889961800203-0.1493666162970.02876944679050.3643793319370.00507430641995-0.1472497191080.365672945469-0.001991048437840.403335283892-68.7777359798-24.0205947711-8.64506125722
152.442678835071.289417864870.05049896143052.50864181045-0.7017843143290.953872077671-0.1940214453990.01871031936580.321846438687-0.009477166687060.1492551827740.303109889962-0.15819061399-0.1947813452150.04675257957360.3571652046110.0700835093815-0.1206447218110.327717181363-0.05251077045040.356504452167-69.7619379503-20.1445509017-4.78143520607
163.483521320463.757202797680.07353789116834.65763016044-0.1083561965531.53148668732-0.3378516801790.658703059059-0.347911485829-0.4045077228740.343904989333-0.1685773748050.1518737344170.2794813769420.02899383624420.3343347007490.0917826733679-0.06685840800090.560175702566-0.1018699276430.45525691925525.0003945638-44.019527061427.413214466
170.8198438661162.053812055730.6185183072249.60313382371-0.01144036178630.299006112087-0.04323409830540.324980535494-0.1456447832020.4225719030110.122845603449-1.107448061330.3072277431380.110308455829-0.1463034040860.4133167148230.0939380640161-0.1385615046860.521591533407-0.04041156210110.51621916559922.9819437009-46.88072870740.4193088334
182.962683186530.924774098536-0.3623181245430.6836425213210.2774425543640.504965171318-0.2388430017770.4910573357180.657527249997-0.1133195699610.1397771251580.128607058385-0.257394089132-0.03037692842010.106786771490.4154025060270.0126956496437-0.1860574019640.3714536836220.01621089541380.50730101512512.7147192301-26.967329385336.1737837863
190.7567349552850.2198962349540.234864614550.8561381774070.007426508005151.192771840050.06761340550820.00222092165936-0.1379645673490.02466474352880.01527359844240.06045445689280.0667678185727-0.15988858321-0.09157453634520.305963528644-0.0141042194421-0.1114624994080.374281161535-0.004456749401570.4203280469785.58319640734-47.458845363156.0590841134
204.17195265131-4.116584556650.1824788748854.92831154315-2.031265965684.55583405203-0.07678676751190.202082536168-0.0819450114738-0.4178489452410.1298783368841.06985453920.21215726279-0.824967977985-0.01138999858290.330163525145-0.0780205408141-0.1318414057180.4564958462370.03615228238040.599273219946-14.0086138794-48.497672380952.47236743
212.476204989860.695331304784-0.1236480684731.967199205340.6392610187011.30422611533-0.1253841575140.4236452781710.164117490101-0.434576516680.009302646565030.264377319486-0.168960175484-0.1851204331120.111538016830.3180659014140.00871458263471-0.1293099336090.402506118541-0.002171856704330.3388305981635.89221552008-38.945345373430.8796593798
225.443467421171.76004472844-0.203935400322.35847330473-0.8051431579191.374164116980.2304197376180.111704624268-0.704986308469-0.02114964587420.137133118621-0.08548372557910.430465756658-0.0316332868968-0.4015207140410.447551508330.0323580218517-0.2127979280160.312014001291-0.02549846379260.5804257610039.38918151754-60.215001837255.6477746728
235.005514776511.53271220822-1.624403104281.44319163192-1.244511918061.192487364750.114380636732-0.0655364313407-1.13427695454-0.133523707683-0.103347098161-0.2000719007020.174582409989-0.01591679863840.02185598857940.5108305077360.0352593031413-0.2530601130740.410540664497-0.08182551460930.70050003205742.2828435788-60.886392614762.3232039797
246.80905916841.07471034133-5.70198412418-0.00691293920048-0.8805732434096.13127250899-0.1587938975330.0812242306808-0.0990979857352-0.03990463686120.133375701317-0.102910418910.7043734330550.1134688912570.05813832745810.4621133093830.0619601140315-0.2065663178290.46973215298-0.03807334311680.61350969671638.619549725-49.264999968956.244921436
251.20473883957-0.07601972827250.6596300759480.908738381292-0.06304268673980.934054046766-0.0207701155715-0.03670073686840.1094342782710.330121330369-0.0177566070861-0.258547460881-0.1371652461850.1494798037820.05539712276030.3466902452780.00810708003112-0.1761835031290.348276020551-0.02400112818840.47082175723838.6219117156-26.99752626463.0263212735
261.40887241640.06656940246660.7960256957270.432486342732-0.2900129706441.583627654290.00600178088266-0.0127756097610.04975689266870.207179175924-0.0402036647733-0.280987714433-0.01600757726630.2253322757030.02820129729350.3761824822720.0362488636492-0.1767836969680.335799835624-0.03868125678420.5372918416148.5499402919-37.068000816264.8451319873
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 229 )
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 295 )
6X-RAY DIFFRACTION6chain 'A' and (resid 296 through 390 )
7X-RAY DIFFRACTION7chain 'A' and (resid 391 through 428 )
8X-RAY DIFFRACTION8chain 'A' and (resid 429 through 535 )
9X-RAY DIFFRACTION9chain 'A' and (resid 536 through 583 )
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 105A)
11X-RAY DIFFRACTION11chain 'B' and (resid 106 through 138 )
12X-RAY DIFFRACTION12chain 'B' and (resid 139 through 269 )
13X-RAY DIFFRACTION13chain 'B' and (resid 270 through 319 )
14X-RAY DIFFRACTION14chain 'B' and (resid 320 through 485 )
15X-RAY DIFFRACTION15chain 'B' and (resid 486 through 583 )
16X-RAY DIFFRACTION16chain 'C' and (resid 33 through 105A)
17X-RAY DIFFRACTION17chain 'C' and (resid 106 through 138 )
18X-RAY DIFFRACTION18chain 'C' and (resid 139 through 181 )
19X-RAY DIFFRACTION19chain 'C' and (resid 182 through 393 )
20X-RAY DIFFRACTION20chain 'C' and (resid 394 through 428 )
21X-RAY DIFFRACTION21chain 'C' and (resid 429 through 535 )
22X-RAY DIFFRACTION22chain 'C' and (resid 536 through 583 )
23X-RAY DIFFRACTION23chain 'D' and (resid 33 through 105A)
24X-RAY DIFFRACTION24chain 'D' and (resid 106 through 138 )
25X-RAY DIFFRACTION25chain 'D' and (resid 139 through 346 )
26X-RAY DIFFRACTION26chain 'D' and (resid 347 through 583 )

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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