[日本語] English
万見
- PDB-6bl4: Crystal Complex of Cyclooxygenase-2 with indomethacin-ethylenedia... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 6bl4
タイトルCrystal Complex of Cyclooxygenase-2 with indomethacin-ethylenediamine-dansyl conjugate
要素Prostaglandin G/H synthase 2
キーワードOXIDOREDUCTASE/INHIBITOR / protein-inhibitor complex / fluorescent inhibitor / 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 / positive regulation of platelet-derived growth factor production / hair cycle / cellular response to homocysteine / : ...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 / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / positive regulation of fibroblast growth factor production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / positive regulation of transforming growth factor beta production / cellular response to lead ion / negative regulation of synaptic transmission, dopaminergic / 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 / response to fatty acid / response to fructose / positive regulation of smooth muscle contraction / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / positive regulation of fever generation / prostaglandin secretion / response to vitamin D / cellular response to fluid shear stress / response to selenium ion / response to nematode / nuclear outer membrane / response to angiotensin / nuclear inner membrane / response to manganese ion / prostaglandin biosynthetic process / negative regulation of smooth muscle contraction / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to ATP / maintenance of blood-brain barrier / bone mineralization / negative regulation of calcium ion transport / negative regulation of cell cycle / decidualization / response to tumor necrosis factor / positive regulation of vascular endothelial growth factor production / 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 / positive regulation of smooth muscle cell proliferation / peroxidase activity / caveola / regulation of blood pressure / memory / positive regulation of protein import into nucleus / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / response to estradiol / regulation of cell population proliferation / cellular response to heat / cellular response to lipopolysaccharide / angiogenesis / cellular response to hypoxia / response to oxidative stress / neuron projection / positive regulation of apoptotic process / response to xenobiotic stimulus / negative regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / 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
Chem-DXS / PROTOPORPHYRIN IX CONTAINING FE / 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: 2.22 Å
データ登録者Xu, S. / Uddin, M.J. / Banerjee, S. / Marnett, L.J.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 米国
National Institutes of Health/National Cancer Institute (NIH/NCI) 米国
引用ジャーナル: J.Biol.Chem. / 年: 2019
タイトル: Fluorescent indomethacin-dansyl conjugates utilize the membrane-binding domain of cyclooxygenase-2 to block the opening to the active site.
著者: Xu, S. / Uddin, M.J. / Banerjee, S. / Duggan, K. / Musee, J. / Kiefer, J.R. / Ghebreselasie, K. / Rouzer, C.A. / Marnett, L.J.
履歴
登録2017年11月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年11月14日Provider: repository / タイプ: Initial release
改定 1.12019年2月20日Group: Author supporting evidence / Data collection / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22019年3月13日Group: Data collection / カテゴリ: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
改定 1.32019年5月15日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.42019年6月12日Group: Data collection / 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_author.identifier_ORCID
改定 1.52019年12月4日Group: Author supporting evidence / カテゴリ: pdbx_audit_support
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.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_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 2.12023年10月4日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 2.22024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

-
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

-
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)279,25929
ポリマ－269,3314
非ポリマー9,92825
水25,8341434
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)139,48314
ポリマ－134,6652
非ポリマー4,81812
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-15 kcal/mol
Surface area41670 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)139,77515
ポリマ－134,6652
非ポリマー5,11013
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-12 kcal/mol
Surface area41700 Å2
手法PISA
単位格子
Length a, b, c (Å)214.795, 120.414, 134.417
Angle α, β, γ (deg.)90.000, 123.600, 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
11chain A
21chain B
31chain C
41chain D

NCSドメイン領域:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 33 - 583 / Label seq-ID: 1 - 552

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

-
要素

-
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
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q05769, prostaglandin-endoperoxide synthase

-
糖 , 3種, 17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
#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 / 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: 5 / 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

-
非ポリマー , 3種, 1442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
#5: 化合物
ChemComp-DXS / 2-[1-(4-chlorobenzene-1-carbonyl)-5-methoxy-2-methyl-1H-indol-3-yl]-N-[2-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)ethyl]acetamide


分子量: 633.157 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C33H33ClN4O5S
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1434 / 由来タイプ: 天然 / 式: H2O

-
詳細

Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.85 Å3/Da / 溶媒含有率: 56.85 %
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

-
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: 0.97918 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年6月24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: 0.97918 Å / 相対比: 1
反射解像度: 2.22→111.96 Å / Num. obs: 138444 / % possible obs: 98.7 % / 冗長度: 2.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.093 / Rrim(I) all: 0.144 / Net I/σ(I): 9.3 / Num. measured all: 325121 / Scaling rejects: 1
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.22-2.342.40.677200050.5550.5660.88697.9
7.02-111.962.30.02745420.9970.0240.03699.3

-
解析

ソフトウェア
名称バージョン分類
Aimless0.1.27データスケーリング
PHENIX1.12_2829精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3nt1

3nt1


解像度: 2.22→111.959 Å / SU ML: 0.25 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 22.61
Rfactor反射数%反射
Rfree0.2195 4148 3 %
Rwork0.1886 --
obs0.1895 138373 98.47 %
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 max: 97.2 Å2 / Biso mean: 35.7512 Å2 / Biso min: 12.84 Å2
精密化ステップサイクル: final / 解像度: 2.22→111.959 Å
タンパク質核酸リガンド溶媒全体
原子数17896 0 672 1446 20014
Biso mean--43.49 38.12 -
残基数----2208
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01219161
X-RAY DIFFRACTIONf_angle_d1.01326081
X-RAY DIFFRACTIONf_chiral_restr0.22753
X-RAY DIFFRACTIONf_plane_restr0.0063320
X-RAY DIFFRACTIONf_dihedral_angle_d19.6187107
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A11073X-RAY DIFFRACTION4.974TORSIONAL
12B11073X-RAY DIFFRACTION4.974TORSIONAL
13C11073X-RAY DIFFRACTION4.974TORSIONAL
14D11073X-RAY DIFFRACTION4.974TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.24520.33961390.28274395453497
2.2452-2.27160.29891410.27534427456898
2.2716-2.29940.29041300.26764429455998
2.2994-2.32850.30371320.2644435456798
2.3285-2.35910.30291500.25924467461798
2.3591-2.39140.31481360.24834393452998
2.3914-2.42560.25761340.24344426456098
2.4256-2.46180.29881490.24244457460698
2.4618-2.50030.27171310.23194462459398
2.5003-2.54130.2661320.22344427455998
2.5413-2.58510.23911390.22524466460598
2.5851-2.63210.27741390.22244440457998
2.6321-2.68270.2411400.21864495463598
2.6827-2.73750.23551350.21054479461498
2.7375-2.7970.25741410.20724444458598
2.797-2.86210.26061440.21764443458798
2.8621-2.93370.24251380.21114463460199
2.9337-3.0130.20731360.20924473460999
3.013-3.10170.29421280.19864493462199
3.1017-3.20180.23281470.19154478462599
3.2018-3.31620.22211440.19014449459399
3.3162-3.4490.22761350.18394537467299
3.449-3.6060.18571370.17134466460399
3.606-3.79610.17171380.15534486462499
3.7961-4.0340.18241400.15184497463799
4.034-4.34540.15441350.14524528466399
4.3454-4.78270.15931390.13584529466899
4.7827-5.47480.15891420.14254558470099
5.4748-6.89750.21391390.17764575471499
6.8975-112.10140.18641380.174608474699
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)
10.3508-0.34530.86462.0124-1.95753.0195-0.11920.00220.28820.38690.01120.0433-0.95130.23910.15590.4572-0.097-0.13160.3253-0.01920.3708-40.6345-2.455618.2958
24.10930.990.82293.41140.10775.8560.1267-0.20440.17440.2082-0.18040.2696-0.6012-0.48230.0310.4530.02140.03840.301-0.13630.3302-54.1022-17.009638.2308
31.6185-0.15280.71960.8753-0.60262.0059-0.06320.1320.13660.1017-0.1431-0.2528-0.14040.36660.19680.2072-0.0562-0.03760.23520.04040.1929-33.5149-24.959417.8744
41.57060.69780.81784.6751-0.7862.06690.13050.0899-0.239-0.1007-0.0596-0.04860.22440.0698-0.09070.15870.02850.00470.1918-0.00160.1349-48.6742-48.097417.7199
57.3858-0.93220.89022.01170.02361.6915-0.07760.0112-0.43080.0294-0.0034-0.18790.13190.18780.07870.2312-0.00380.00460.11970.03530.1422-44.9788-49.403423.29
61.34410.39230.65311.03020.01461.85860.0924-0.24360.11680.2621-0.1410.0363-0.176-0.1380.0510.2032-0.00510.01140.20450.00060.1349-52.4534-30.683526.2827
75.30191.1887-0.37114.56840.88790.26490.0296-0.5379-0.38870.5238-0.0885-0.46640.19150.55270.03570.33540.0151-0.1010.38940.09920.2471-32.739-48.225735.2705
81.8352-0.44770.44671.113-0.43840.9645-0.0751-0.07930.25350.2878-0.1096-0.306-0.29780.37330.17370.2875-0.0981-0.09660.32960.03230.2468-29.5297-19.534927.0753
92.7349-1.15160.47962.4583-1.68112.0259-0.1135-0.3390.01930.32250.13940.0518-0.1487-0.31960.01890.2368-0.0040.02410.2367-0.02510.109-56.8462-37.640632.0763
101.4277-0.61580.25311.4004-2.1163.8291-0.0357-0.4578-0.03210.37940.4350.6078-0.4239-0.5658-0.42330.240.02640.06150.490.05880.378-81.419-28.17417.7886
113.70310.2104-0.11787.16420.43721.7756-0.1591-0.49450.59930.52580.43880.325-0.29920.1702-0.15660.38140.11950.07010.4316-0.10640.4914-73.9912-4.18555.23
121.8789-0.33091.35820.862-0.44241.93260.1694-0.0698-0.2521-0.14510.21290.34570.3207-0.4247-0.310.2164-0.0878-0.04880.34110.08120.2558-72.3761-38.67523.9951
131.77180.5549-0.05341.2829-0.44451.4414-0.05410.1146-0.0329-0.27360.04740.00310.10440.00460.010.2443-0.0259-0.01540.18180.03720.1403-57.0291-23.9391-13.1453
144.09971.53521.53824.00380.09823.1049-0.25060.6191-0.1035-0.79270.2749-0.085-0.03820.3118-0.03550.2357-0.02970.03910.32160.04860.1399-51.4859-21.3781-18.3133
152.5363-0.09820.58020.9119-0.38421.2167-0.04460.01440.28780.04630.07550.1592-0.1377-0.1012-0.02330.2093-0.003-0.02890.16920.0270.1737-60.4257-14.3954-1.3621
163.720.93-1.8664.3911.53813.3015-0.20010.71440.0572-0.82360.31050.46330.1853-0.3427-0.11660.3978-0.0793-0.09210.36390.06720.2468-65.3417-19.9467-28.2226
171.6040.14370.17821.0549-0.1411.31910.02920.0019-0.0171-0.14510.14860.49070.1318-0.5815-0.13950.2087-0.051-0.07190.41350.11040.3503-81.518-28.418-4.3929
181.3990.44361.50311.2704-0.95564.455-0.29350.13190.3325-0.0302-0.06930.1239-0.55790.10080.31740.28850.023-0.05320.15740.01650.2172-56.2446-7.1151-6.8733
193.17331.2196-0.50510.96470.23521.1576-0.30990.6251-0.3349-0.49060.2257-0.24820.04380.24380.1310.398-0.06850.05420.57-0.02320.2348-79.8775-95.005325.1803
201.88380.33471.01943.6425-0.41663.925-0.12020.0679-0.3183-0.19970.3489-0.34540.49380.533-0.16730.50880.02250.09720.4779-0.2010.3831-90.3398-119.091835.0468
211.85580.74760.14631.2166-0.00290.6851-0.06930.1660.137-0.04710.08230.0793-0.035-0.0262-0.0020.1559-0.00020.00370.19670.03660.1367-99.4391-93.7448.5386
224.4923-2.11881.91034.3703-0.24111.6139-0.0887-0.2721-0.05990.32310.16580.31-0.1321-0.2461-0.05790.2213-0.04450.08270.24670.04730.1223-108.4332-102.167662.3273
231.670.29590.62451.4701-0.19761.65540.06720.0788-0.2221-0.071-0.0028-0.15680.1889-0.0185-0.06360.155-0.01710.0010.1668-0.00460.1695-93.8299-108.995849.8275
242.585-1.1569-1.28485.772-0.49734.1650.00520.3322-0.0109-0.10480.1280.90460.0534-0.6919-0.16090.1921-0.0444-0.00470.3730.06740.262-121.1317-103.581550.9643
250.90950.2895-0.02741.1085-0.08971.1887-0.17760.57530.1391-0.34190.16410.0987-0.007-0.02450.01760.2892-0.083-0.03860.45740.07230.1874-101.5011-94.877230.0215
267.50190.82370.90032.4794-0.38050.87480.18730.1555-0.74370.1007-0.0043-0.09780.147-0.0121-0.19260.207-0.0064-0.02120.156-0.01650.151-98.2589-116.350755.0747
273.62761.7-0.08172.0238-0.14120.02310.0013-0.3248-1.2192-0.1017-0.0513-0.43480.26310.20220.05610.39370.0561-0.16880.36130.06750.6551-70.2931-120.980664.7681
284.4694-0.65440.86492.1085-1.14934.052-0.03310.3887-0.6052-0.2318-0.2064-0.31070.16640.19590.17010.3590.10850.09510.3996-0.10080.641-53.863-106.386847.2067
291.33180.40320.44180.67650.14630.7530.1929-0.4482-0.26130.2624-0.1463-0.30080.0965-0.022-0.0450.2813-0.044-0.12570.29410.07880.2962-69.1043-98.498871.8554
302.16580.5720.54832.5397-0.09931.9778-0.0932-0.03710.25120.2513-0.0285-0.2034-0.3430.08670.11030.1926-0.0141-0.05530.19350.01910.2293-69.4636-74.667558.3845
311.27410.30630.25911.1331-0.31741.00830.0884-0.1511-0.20970.2399-0.1242-0.5120.03880.22960.03670.2189-0.0076-0.08840.28990.03480.3685-59.9462-94.826565.1493
322.39152.09750.08483.30880.31642.264-0.11480.4419-0.2691-0.10980.1833-0.6165-0.02630.4599-0.07290.16030.00390.0680.3257-0.01630.3073-60.4753-85.762545.954
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 93 )A33 - 93
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 123 )A94 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 218 )A124 - 218
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 269 )A219 - 269
5X-RAY DIFFRACTION5chain 'A' and (resid 270 through 319 )A270 - 319
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 390 )A320 - 390
7X-RAY DIFFRACTION7chain 'A' and (resid 391 through 428 )A391 - 428
8X-RAY DIFFRACTION8chain 'A' and (resid 429 through 535 )A429 - 535
9X-RAY DIFFRACTION9chain 'A' and (resid 536 through 583 )A536 - 583
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 93 )B33 - 93
11X-RAY DIFFRACTION11chain 'B' and (resid 94 through 123 )B94 - 123
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 181 )B124 - 181
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 269 )B182 - 269
14X-RAY DIFFRACTION14chain 'B' and (resid 270 through 319 )B270 - 319
15X-RAY DIFFRACTION15chain 'B' and (resid 320 through 390 )B320 - 390
16X-RAY DIFFRACTION16chain 'B' and (resid 391 through 428 )B391 - 428
17X-RAY DIFFRACTION17chain 'B' and (resid 429 through 535 )B429 - 535
18X-RAY DIFFRACTION18chain 'B' and (resid 536 through 583 )B536 - 583
19X-RAY DIFFRACTION19chain 'C' and (resid 33 through 93 )C33 - 93
20X-RAY DIFFRACTION20chain 'C' and (resid 94 through 123 )C94 - 123
21X-RAY DIFFRACTION21chain 'C' and (resid 124 through 269 )C124 - 269
22X-RAY DIFFRACTION22chain 'C' and (resid 270 through 319 )C270 - 319
23X-RAY DIFFRACTION23chain 'C' and (resid 320 through 390 )C320 - 390
24X-RAY DIFFRACTION24chain 'C' and (resid 391 through 428 )C391 - 428
25X-RAY DIFFRACTION25chain 'C' and (resid 429 through 535 )C429 - 535
26X-RAY DIFFRACTION26chain 'C' and (resid 536 through 583 )C536 - 583
27X-RAY DIFFRACTION27chain 'D' and (resid 33 through 93 )D33 - 93
28X-RAY DIFFRACTION28chain 'D' and (resid 94 through 123 )D94 - 123
29X-RAY DIFFRACTION29chain 'D' and (resid 124 through 218 )D124 - 218
30X-RAY DIFFRACTION30chain 'D' and (resid 219 through 319 )D219 - 319
31X-RAY DIFFRACTION31chain 'D' and (resid 320 through 535 )D320 - 535
32X-RAY DIFFRACTION32chain 'D' and (resid 536 through 583 )D536 - 583

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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