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- PDB-6fqj: GluA2(flop) G724C ligand binding core dimer bound to ZK200775 at ... -

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基本情報

登録情報
データベース: PDB / ID: 6fqj
タイトルGluA2(flop) G724C ligand binding core dimer bound to ZK200775 at 2.50 Angstrom resolution
要素Glutamate receptor 2,Glutamate receptor 2
キーワードMEMBRANE PROTEIN / AMPAR receptor / Ligand binding domain / Competitive antagonist / Cross-linked dimer
機能・相同性
機能・相同性情報


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic transmission, glutamatergic / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-ZK1 / Glutamate receptor 2
類似検索 - 構成要素
生物種Rattus norvegicus (ドブネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.50001683981 Å
データ登録者Coombs, I.D. / Soto, D. / Gold, M.G. / Farrant, M.F. / Cull-Candy, S.G.
資金援助 英国, 3件
組織認可番号国
Medical Research Council (United Kingdom)MR/J002976/1 英国
Medical Research Council (United Kingdom)MR/J012998/1 英国
Wellcome Trust086185/Z/08/Z 英国
引用ジャーナル: Nat Commun / 年: 2019
タイトル: Homomeric GluA2(R) AMPA receptors can conduct when desensitized.
著者: Coombs, I.D. / Soto, D. / McGee, T.P. / Gold, M.G. / Farrant, M. / Cull-Candy, S.G.
履歴
登録2018年2月14日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年3月13日Provider: repository / タイプ: Initial release
改定 1.12019年10月2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_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年1月17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 1.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
C: Glutamate receptor 2,Glutamate receptor 2
D: Glutamate receptor 2,Glutamate receptor 2
E: Glutamate receptor 2,Glutamate receptor 2
F: Glutamate receptor 2,Glutamate receptor 2
G: Glutamate receptor 2,Glutamate receptor 2
H: Glutamate receptor 2,Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)237,87316
ポリマ－234,5998
非ポリマー3,2748
水14,862825
1
A: Glutamate receptor 2,Glutamate receptor 2
H: Glutamate receptor 2,Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,4684
ポリマ－58,6502
非ポリマー8192
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-14 kcal/mol
Surface area24230 Å2
手法PISA
2
B: Glutamate receptor 2,Glutamate receptor 2
G: Glutamate receptor 2,Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,4684
ポリマ－58,6502
非ポリマー8192
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-15 kcal/mol
Surface area23860 Å2
手法PISA
3
C: Glutamate receptor 2,Glutamate receptor 2
E: Glutamate receptor 2,Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,4684
ポリマ－58,6502
非ポリマー8192
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-15 kcal/mol
Surface area23860 Å2
手法PISA
4
D: Glutamate receptor 2,Glutamate receptor 2
F: Glutamate receptor 2,Glutamate receptor 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,4684
ポリマ－58,6502
非ポリマー8192
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-15 kcal/mol
Surface area23610 Å2
手法PISA
単位格子
Length a, b, c (Å)86.010, 144.290, 199.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81

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
11THRTHRHISHIS(chain 'A' and (resid 5 through 23 or resid 26...AA5 - 235 - 23
12LEULEUALAALA(chain 'A' and (resid 5 through 23 or resid 26...AA26 - 4426 - 44
13HISHISALAALA(chain 'A' and (resid 5 through 23 or resid 26...AA46 - 6346 - 63
14ASPASPALAALA(chain 'A' and (resid 5 through 23 or resid 26...AA65 - 6665 - 66
15THRTHRTHRTHR(chain 'A' and (resid 5 through 23 or resid 26...AA6868
16ILEILEILEILE(chain 'A' and (resid 5 through 23 or resid 26...AA70 - 12170 - 121
17SERSERSERSER(chain 'A' and (resid 5 through 23 or resid 26...AA123 - 128123 - 128
18GLNGLNTHRTHR(chain 'A' and (resid 5 through 23 or resid 26...AA130 - 131130 - 131
19ILEILEPHEPHE(chain 'A' and (resid 5 through 23 or resid 26...AA133 - 147133 - 147
110SERSERSERSER(chain 'A' and (resid 5 through 23 or resid 26...AA150150
111ILEILEMETMET(chain 'A' and (resid 5 through 23 or resid 26...AA152 - 162152 - 162
112SERSERVALVAL(chain 'A' and (resid 5 through 23 or resid 26...AA164 - 171164 - 171
113THRTHRARGARG(chain 'A' and (resid 5 through 23 or resid 26...AA173 - 182173 - 182
114SERSERLYSLYS(chain 'A' and (resid 5 through 23 or resid 26...AA184 - 185184 - 185
115TYRTYRLEULEU(chain 'A' and (resid 5 through 23 or resid 26...AA188 - 192188 - 192
116SERSERARGARG(chain 'A' and (resid 5 through 23 or resid 26...AA194 - 203194 - 203
117PROPROTHRTHR(chain 'A' and (resid 5 through 23 or resid 26...AA205 - 208205 - 208
118LYSLYSSERSER(chain 'A' and (resid 5 through 23 or resid 26...AA210 - 217210 - 217
119GLYGLYGLUGLU(chain 'A' and (resid 5 through 23 or resid 26...AA219 - 243219 - 243
120GLYGLYTYRTYR(chain 'A' and (resid 5 through 23 or resid 26...AA245 - 256245 - 256
121GLYGLYCYSCYS(chain 'A' and (resid 5 through 23 or resid 26...AA259 - 261259 - 261
222THRTHRHISHIS(chain 'B' and (resid 5 through 23 or resid 26...BB5 - 235 - 23
223LEULEUALAALA(chain 'B' and (resid 5 through 23 or resid 26...BB26 - 4426 - 44
224HISHISALAALA(chain 'B' and (resid 5 through 23 or resid 26...BB46 - 6346 - 63
225ASPASPALAALA(chain 'B' and (resid 5 through 23 or resid 26...BB65 - 6665 - 66
226THRTHRTHRTHR(chain 'B' and (resid 5 through 23 or resid 26...BB6868
227ILEILEILEILE(chain 'B' and (resid 5 through 23 or resid 26...BB70 - 12170 - 121
228SERSERSERSER(chain 'B' and (resid 5 through 23 or resid 26...BB123 - 128123 - 128
229GLNGLNTHRTHR(chain 'B' and (resid 5 through 23 or resid 26...BB130 - 131130 - 131
230ILEILEPHEPHE(chain 'B' and (resid 5 through 23 or resid 26...BB133 - 147133 - 147
231SERSERSERSER(chain 'B' and (resid 5 through 23 or resid 26...BB150150
232ILEILEMETMET(chain 'B' and (resid 5 through 23 or resid 26...BB152 - 162152 - 162
233SERSERVALVAL(chain 'B' and (resid 5 through 23 or resid 26...BB164 - 171164 - 171
234THRTHRARGARG(chain 'B' and (resid 5 through 23 or resid 26...BB173 - 182173 - 182
235SERSERLYSLYS(chain 'B' and (resid 5 through 23 or resid 26...BB184 - 185184 - 185
236TYRTYRLEULEU(chain 'B' and (resid 5 through 23 or resid 26...BB188 - 192188 - 192
237SERSERARGARG(chain 'B' and (resid 5 through 23 or resid 26...BB194 - 203194 - 203
238PROPROTHRTHR(chain 'B' and (resid 5 through 23 or resid 26...BB205 - 208205 - 208
239LYSLYSSERSER(chain 'B' and (resid 5 through 23 or resid 26...BB210 - 217210 - 217
240GLYGLYGLUGLU(chain 'B' and (resid 5 through 23 or resid 26...BB219 - 243219 - 243
241GLYGLYTYRTYR(chain 'B' and (resid 5 through 23 or resid 26...BB245 - 256245 - 256
242GLYGLYCYSCYS(chain 'B' and (resid 5 through 23 or resid 26...BB259 - 261259 - 261
343THRTHRHISHIS(chain 'C' and (resid 5 through 23 or resid 26...CC5 - 235 - 23
344LEULEUALAALA(chain 'C' and (resid 5 through 23 or resid 26...CC26 - 4426 - 44
345HISHISALAALA(chain 'C' and (resid 5 through 23 or resid 26...CC46 - 6346 - 63
346ASPASPALAALA(chain 'C' and (resid 5 through 23 or resid 26...CC65 - 6665 - 66
347THRTHRTHRTHR(chain 'C' and (resid 5 through 23 or resid 26...CC6868
348ILEILEILEILE(chain 'C' and (resid 5 through 23 or resid 26...CC70 - 12170 - 121
349SERSERSERSER(chain 'C' and (resid 5 through 23 or resid 26...CC123 - 128123 - 128
350GLNGLNTHRTHR(chain 'C' and (resid 5 through 23 or resid 26...CC130 - 131130 - 131
351ILEILEPHEPHE(chain 'C' and (resid 5 through 23 or resid 26...CC133 - 147133 - 147
352SERSERSERSER(chain 'C' and (resid 5 through 23 or resid 26...CC150150
353ILEILEMETMET(chain 'C' and (resid 5 through 23 or resid 26...CC152 - 162152 - 162
354SERSERVALVAL(chain 'C' and (resid 5 through 23 or resid 26...CC164 - 171164 - 171
355THRTHRARGARG(chain 'C' and (resid 5 through 23 or resid 26...CC173 - 182173 - 182
356SERSERLYSLYS(chain 'C' and (resid 5 through 23 or resid 26...CC184 - 185184 - 185
357TYRTYRLEULEU(chain 'C' and (resid 5 through 23 or resid 26...CC188 - 192188 - 192
358SERSERARGARG(chain 'C' and (resid 5 through 23 or resid 26...CC194 - 203194 - 203
359PROPROTHRTHR(chain 'C' and (resid 5 through 23 or resid 26...CC205 - 208205 - 208
360LYSLYSSERSER(chain 'C' and (resid 5 through 23 or resid 26...CC210 - 217210 - 217
361GLYGLYGLUGLU(chain 'C' and (resid 5 through 23 or resid 26...CC219 - 243219 - 243
362GLYGLYTYRTYR(chain 'C' and (resid 5 through 23 or resid 26...CC245 - 256245 - 256
363GLYGLYCYSCYS(chain 'C' and (resid 5 through 23 or resid 26...CC259 - 261259 - 261
464THRTHRHISHIS(chain 'D' and (resid 5 through 20 or (resid 21...DD5 - 235 - 23
465LEULEUALAALA(chain 'D' and (resid 5 through 20 or (resid 21...DD26 - 4426 - 44
466HISHISALAALA(chain 'D' and (resid 5 through 20 or (resid 21...DD46 - 6346 - 63
467ASPASPALAALA(chain 'D' and (resid 5 through 20 or (resid 21...DD65 - 6665 - 66
468THRTHRTHRTHR(chain 'D' and (resid 5 through 20 or (resid 21...DD6868
469ILEILEILEILE(chain 'D' and (resid 5 through 20 or (resid 21...DD70 - 12170 - 121
470SERSERSERSER(chain 'D' and (resid 5 through 20 or (resid 21...DD123 - 128123 - 128
471GLNGLNTHRTHR(chain 'D' and (resid 5 through 20 or (resid 21...DD130 - 131130 - 131
472ILEILEPHEPHE(chain 'D' and (resid 5 through 20 or (resid 21...DD133 - 147133 - 147
473SERSERSERSER(chain 'D' and (resid 5 through 20 or (resid 21...DD150150
474ILEILEMETMET(chain 'D' and (resid 5 through 20 or (resid 21...DD152 - 162152 - 162
475SERSERVALVAL(chain 'D' and (resid 5 through 20 or (resid 21...DD164 - 171164 - 171
476THRTHRARGARG(chain 'D' and (resid 5 through 20 or (resid 21...DD173 - 182173 - 182
477SERSERLYSLYS(chain 'D' and (resid 5 through 20 or (resid 21...DD184 - 185184 - 185
478TYRTYRLEULEU(chain 'D' and (resid 5 through 20 or (resid 21...DD188 - 192188 - 192
479SERSERARGARG(chain 'D' and (resid 5 through 20 or (resid 21...DD194 - 203194 - 203
480PROPROTHRTHR(chain 'D' and (resid 5 through 20 or (resid 21...DD205 - 208205 - 208
481LYSLYSSERSER(chain 'D' and (resid 5 through 20 or (resid 21...DD210 - 217210 - 217
482GLYGLYGLUGLU(chain 'D' and (resid 5 through 20 or (resid 21...DD219 - 243219 - 243
483GLYGLYTYRTYR(chain 'D' and (resid 5 through 20 or (resid 21...DD245 - 256245 - 256
484GLYGLYCYSCYS(chain 'D' and (resid 5 through 20 or (resid 21...DD259 - 261259 - 261
585THRTHRHISHIS(chain 'E' and (resid 5 through 20 or (resid 21...EE5 - 235 - 23
586LEULEUALAALA(chain 'E' and (resid 5 through 20 or (resid 21...EE26 - 4426 - 44
587HISHISALAALA(chain 'E' and (resid 5 through 20 or (resid 21...EE46 - 6346 - 63
588ASPASPALAALA(chain 'E' and (resid 5 through 20 or (resid 21...EE65 - 6665 - 66
589THRTHRTHRTHR(chain 'E' and (resid 5 through 20 or (resid 21...EE6868
590ILEILEILEILE(chain 'E' and (resid 5 through 20 or (resid 21...EE70 - 12170 - 121
591SERSERSERSER(chain 'E' and (resid 5 through 20 or (resid 21...EE123 - 128123 - 128
592GLNGLNTHRTHR(chain 'E' and (resid 5 through 20 or (resid 21...EE130 - 131130 - 131
593ILEILEPHEPHE(chain 'E' and (resid 5 through 20 or (resid 21...EE133 - 147133 - 147
594SERSERSERSER(chain 'E' and (resid 5 through 20 or (resid 21...EE150150
595ILEILEMETMET(chain 'E' and (resid 5 through 20 or (resid 21...EE152 - 162152 - 162
596SERSERVALVAL(chain 'E' and (resid 5 through 20 or (resid 21...EE164 - 171164 - 171
597THRTHRARGARG(chain 'E' and (resid 5 through 20 or (resid 21...EE173 - 182173 - 182
598SERSERLYSLYS(chain 'E' and (resid 5 through 20 or (resid 21...EE184 - 185184 - 185
599TYRTYRLEULEU(chain 'E' and (resid 5 through 20 or (resid 21...EE188 - 192188 - 192
5100SERSERARGARG(chain 'E' and (resid 5 through 20 or (resid 21...EE194 - 203194 - 203
5101PROPROTHRTHR(chain 'E' and (resid 5 through 20 or (resid 21...EE205 - 208205 - 208
5102LYSLYSSERSER(chain 'E' and (resid 5 through 20 or (resid 21...EE210 - 217210 - 217
5103GLYGLYGLUGLU(chain 'E' and (resid 5 through 20 or (resid 21...EE219 - 243219 - 243
5104GLYGLYTYRTYR(chain 'E' and (resid 5 through 20 or (resid 21...EE245 - 256245 - 256
5105GLYGLYCYSCYS(chain 'E' and (resid 5 through 20 or (resid 21...EE259 - 261259 - 261
6106THRTHRHISHIS(chain 'F' and (resid 5 through 23 or resid 26...FF5 - 235 - 23
6107LEULEUALAALA(chain 'F' and (resid 5 through 23 or resid 26...FF26 - 4426 - 44
6108HISHISALAALA(chain 'F' and (resid 5 through 23 or resid 26...FF46 - 6346 - 63
6109ASPASPALAALA(chain 'F' and (resid 5 through 23 or resid 26...FF65 - 6665 - 66
6110THRTHRTHRTHR(chain 'F' and (resid 5 through 23 or resid 26...FF6868
6111ILEILEILEILE(chain 'F' and (resid 5 through 23 or resid 26...FF70 - 12170 - 121
6112SERSERSERSER(chain 'F' and (resid 5 through 23 or resid 26...FF123 - 128123 - 128
6113GLNGLNTHRTHR(chain 'F' and (resid 5 through 23 or resid 26...FF130 - 131130 - 131
6114ILEILEPHEPHE(chain 'F' and (resid 5 through 23 or resid 26...FF133 - 147133 - 147
6115SERSERSERSER(chain 'F' and (resid 5 through 23 or resid 26...FF150150
6116ILEILEMETMET(chain 'F' and (resid 5 through 23 or resid 26...FF152 - 162152 - 162
6117SERSERVALVAL(chain 'F' and (resid 5 through 23 or resid 26...FF164 - 171164 - 171
6118THRTHRARGARG(chain 'F' and (resid 5 through 23 or resid 26...FF173 - 182173 - 182
6119SERSERLYSLYS(chain 'F' and (resid 5 through 23 or resid 26...FF184 - 185184 - 185
6120TYRTYRLEULEU(chain 'F' and (resid 5 through 23 or resid 26...FF188 - 192188 - 192
6121SERSERARGARG(chain 'F' and (resid 5 through 23 or resid 26...FF194 - 203194 - 203
6122PROPROTHRTHR(chain 'F' and (resid 5 through 23 or resid 26...FF205 - 208205 - 208
6123LYSLYSSERSER(chain 'F' and (resid 5 through 23 or resid 26...FF210 - 217210 - 217
6124GLYGLYGLUGLU(chain 'F' and (resid 5 through 23 or resid 26...FF219 - 243219 - 243
6125GLYGLYTYRTYR(chain 'F' and (resid 5 through 23 or resid 26...FF245 - 256245 - 256
6126GLYGLYCYSCYS(chain 'F' and (resid 5 through 23 or resid 26...FF259 - 261259 - 261
7127THRTHRHISHIS(chain 'G' and (resid 5 through 20 or (resid 21...GG5 - 235 - 23
7128LEULEUALAALA(chain 'G' and (resid 5 through 20 or (resid 21...GG26 - 4426 - 44
7129HISHISALAALA(chain 'G' and (resid 5 through 20 or (resid 21...GG46 - 6346 - 63
7130ASPASPALAALA(chain 'G' and (resid 5 through 20 or (resid 21...GG65 - 6665 - 66
7131THRTHRTHRTHR(chain 'G' and (resid 5 through 20 or (resid 21...GG6868
7132ILEILEILEILE(chain 'G' and (resid 5 through 20 or (resid 21...GG70 - 12170 - 121
7133SERSERSERSER(chain 'G' and (resid 5 through 20 or (resid 21...GG123 - 128123 - 128
7134GLNGLNTHRTHR(chain 'G' and (resid 5 through 20 or (resid 21...GG130 - 131130 - 131
7135ILEILEPHEPHE(chain 'G' and (resid 5 through 20 or (resid 21...GG133 - 147133 - 147
7136SERSERSERSER(chain 'G' and (resid 5 through 20 or (resid 21...GG150150
7137ILEILEMETMET(chain 'G' and (resid 5 through 20 or (resid 21...GG152 - 162152 - 162
7138SERSERVALVAL(chain 'G' and (resid 5 through 20 or (resid 21...GG164 - 171164 - 171
7139THRTHRARGARG(chain 'G' and (resid 5 through 20 or (resid 21...GG173 - 182173 - 182
7140SERSERLYSLYS(chain 'G' and (resid 5 through 20 or (resid 21...GG184 - 185184 - 185
7141TYRTYRLEULEU(chain 'G' and (resid 5 through 20 or (resid 21...GG188 - 192188 - 192
7142SERSERARGARG(chain 'G' and (resid 5 through 20 or (resid 21...GG194 - 203194 - 203
7143PROPROTHRTHR(chain 'G' and (resid 5 through 20 or (resid 21...GG205 - 208205 - 208
7144LYSLYSSERSER(chain 'G' and (resid 5 through 20 or (resid 21...GG210 - 217210 - 217
7145GLYGLYGLUGLU(chain 'G' and (resid 5 through 20 or (resid 21...GG219 - 243219 - 243
7146GLYGLYTYRTYR(chain 'G' and (resid 5 through 20 or (resid 21...GG245 - 256245 - 256
7147GLYGLYCYSCYS(chain 'G' and (resid 5 through 20 or (resid 21...GG259 - 261259 - 261
8148THRTHRHISHIS(chain 'H' and (resid 5 through 20 or (resid 21...HH5 - 235 - 23
8149LEULEUALAALA(chain 'H' and (resid 5 through 20 or (resid 21...HH26 - 4426 - 44
8150HISHISALAALA(chain 'H' and (resid 5 through 20 or (resid 21...HH46 - 6346 - 63
8151ASPASPALAALA(chain 'H' and (resid 5 through 20 or (resid 21...HH65 - 6665 - 66
8152THRTHRTHRTHR(chain 'H' and (resid 5 through 20 or (resid 21...HH6868
8153ILEILEILEILE(chain 'H' and (resid 5 through 20 or (resid 21...HH70 - 12170 - 121
8154SERSERSERSER(chain 'H' and (resid 5 through 20 or (resid 21...HH123 - 128123 - 128
8155GLNGLNTHRTHR(chain 'H' and (resid 5 through 20 or (resid 21...HH130 - 131130 - 131
8156ILEILEPHEPHE(chain 'H' and (resid 5 through 20 or (resid 21...HH133 - 147133 - 147
8157SERSERSERSER(chain 'H' and (resid 5 through 20 or (resid 21...HH150150
8158ILEILEMETMET(chain 'H' and (resid 5 through 20 or (resid 21...HH152 - 162152 - 162
8159SERSERVALVAL(chain 'H' and (resid 5 through 20 or (resid 21...HH164 - 171164 - 171
8160THRTHRARGARG(chain 'H' and (resid 5 through 20 or (resid 21...HH173 - 182173 - 182
8161SERSERLYSLYS(chain 'H' and (resid 5 through 20 or (resid 21...HH184 - 185184 - 185
8162TYRTYRLEULEU(chain 'H' and (resid 5 through 20 or (resid 21...HH188 - 192188 - 192
8163SERSERARGARG(chain 'H' and (resid 5 through 20 or (resid 21...HH194 - 203194 - 203
8164PROPROTHRTHR(chain 'H' and (resid 5 through 20 or (resid 21...HH205 - 208205 - 208
8165LYSLYSSERSER(chain 'H' and (resid 5 through 20 or (resid 21...HH210 - 217210 - 217
8166GLYGLYGLUGLU(chain 'H' and (resid 5 through 20 or (resid 21...HH219 - 243219 - 243
8167GLYGLYTYRTYR(chain 'H' and (resid 5 through 20 or (resid 21...HH245 - 256245 - 256
8168GLYGLYCYSCYS(chain 'H' and (resid 5 through 20 or (resid 21...HH259 - 261259 - 261

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要素

#1: タンパク質
Glutamate receptor 2,Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


分子量: 29324.826 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Gria2, Glur2 / プラスミド: pET22b / 発現宿主: Escherichia coli K-12 (大腸菌) / 株 (発現宿主): Origami B / 参照: UniProt: P19491
#2: 化合物
ChemComp-ZK1 / {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / [[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid / ZK-200775


分子量: 409.254 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C14H15F3N3O6P / コメント: アンタゴニスト, 薬剤*YM
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 825 / 由来タイプ: 天然 / 式: H2O
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: 2.62 Å3/Da / 溶媒含有率: 53.08 %
結晶化温度: 287 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.2M Ammonium Chloride, 20% PEG 3350, 10microM ZK200775.

-
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: Diamond / ビームライン: I24 / 波長: 0.9686 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2017年1月13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: 0.9686 Å / 相対比: 1
反射解像度: 2.258769→81.83 Å / Num. obs: 114724 / % possible obs: 99.9 % / 冗長度: 1.9 % / CC1/2: 0.985 / Rpim(I) all: 0.086 / Rrim(I) all: 0.121 / Net I/σ(I): 6.8
反射 シェル解像度: 2.26→2.34 Å

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
Aimlessデータスケーリング
PHASER位相決定
xia2データ削減
精密化構造決定の手法: 分子置換
開始モデル: 3KGC

3kgc


解像度: 2.50001683981→81.83 Å / SU ML: 0.351067286516 / 交差検証法: FREE R-VALUE / σ(F): 1.33646103558 / 位相誤差: 27.6175650896
Rfactor反射数%反射
Rfree0.264914925023 8191 4.98505882138 %
Rwork0.197587956151 --
obs0.2009259541 86340 99.1665258431 %
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: 55.2256097443 Å2
精密化ステップサイクル: LAST / 解像度: 2.50001683981→81.83 Å
タンパク質核酸リガンド溶媒全体
原子数16159 0 216 825 17200
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01259804673616691
X-RAY DIFFRACTIONf_angle_d1.2736999694922514
X-RAY DIFFRACTIONf_chiral_restr0.06239347720732457
X-RAY DIFFRACTIONf_plane_restr0.007886230020142778
X-RAY DIFFRACTIONf_dihedral_angle_d15.717416709410064
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.3128904394822920.2761443724725282X-RAY DIFFRACTION99.4824201321
2.5284-2.55820.3228318062452800.2568489536545152X-RAY DIFFRACTION99.7246190564
2.5582-2.58940.335070223612440.2621736895625293X-RAY DIFFRACTION99.7298270893
2.5894-2.62220.3420906945012770.2748481006285211X-RAY DIFFRACTION99.4383040406
2.6222-2.65670.3366498010092950.2803362857415210X-RAY DIFFRACTION99.3323709852
2.6567-2.69310.349143323532810.2791861617635026X-RAY DIFFRACTION96.6490621016
2.6931-2.73150.317400195242700.2459455879715206X-RAY DIFFRACTION99.5455371751
2.7315-2.77230.2946438864082460.2442478326845333X-RAY DIFFRACTION99.6072129977
2.7723-2.81560.3294366865182450.2550368367135144X-RAY DIFFRACTION99.5198522622
2.8156-2.86180.3717882878332760.2506886143725267X-RAY DIFFRACTION99.1947029349
2.8618-2.91110.3107834314092820.2473247553835152X-RAY DIFFRACTION99.4145627516
2.9111-2.96410.3003993957813050.2436880169315231X-RAY DIFFRACTION99.2292525542
2.9641-3.02110.3131163613992580.241470608845209X-RAY DIFFRACTION99.3819305581
3.0211-3.08280.3362492070682640.2386353544135228X-RAY DIFFRACTION99.2948833846
3.0828-3.14980.2946913387662740.2229237027545187X-RAY DIFFRACTION99.4717668488
3.1498-3.22310.3169016286512890.2160730536765223X-RAY DIFFRACTION99.0654205607
3.2231-3.30370.27615565693250.2070141477295193X-RAY DIFFRACTION99.4234234234
3.3037-3.3930.3077049260032600.2033733278055197X-RAY DIFFRACTION99.4895168642
3.393-3.49280.2769294979822550.2054651999215124X-RAY DIFFRACTION97.2694394213
3.4928-3.60560.2377411602252820.1891146446835209X-RAY DIFFRACTION99.5467730239
3.6056-3.73440.2740340709863210.1878520109795100X-RAY DIFFRACTION98.0289330922
3.7344-3.8840.2671213417022770.1856422547795190X-RAY DIFFRACTION99.273651716
3.884-4.06070.216050193772390.1656170477435139X-RAY DIFFRACTION97.4981870921
4.0607-4.27480.2324107155112230.1435626771575289X-RAY DIFFRACTION99.5844625113
4.2748-4.54260.1702332518722180.1300726070445297X-RAY DIFFRACTION99.2978033849
4.5426-4.89330.1960712398152920.1375402498155125X-RAY DIFFRACTION99.4127362819
4.8933-5.38570.2143234947172880.1537829140055265X-RAY DIFFRACTION99.5518106848
5.3857-6.16480.2617843607252560.1962597691615236X-RAY DIFFRACTION99.8001090314
6.1648-7.7660.2382252024942690.1689616991135239X-RAY DIFFRACTION99.6923076923
7.766-82.00670.1832130559473080.1680018670275163X-RAY DIFFRACTION99.1841914431
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)
11.67890191098-0.6455034607810.3965018951030.659199437124-0.1747363061030.6620134583960.03302236399440.03420531878070.1676751406120.0341441365049-0.0591518658916-0.00702850791983-0.0507862573689-0.1242465234710.08066492942460.303989684737-0.01743916267210.03437663253920.287707284572-0.05064060526930.2598067667714.2308009147224.901720973320.4962830987
20.822745659357-0.626024042307-0.4772225476183.739676978630.6668062678782.483626103280.0153732770424-0.032659138956-0.1356500624770.190898480875-0.19021302061-0.07565955000320.2478135310140.009865269622840.1386547960230.322511568876-0.02597567873670.001487447778250.2824939290740.02640084121010.23998146448519.390770433313.850706164335.5340113928
31.219651435430.4821008619160.2456690136212.310663171910.7475073404634.251198006760.01048500867090.06057200233220.0521289877416-0.190637201438-0.104138365831-0.294613679559-0.0976502055606-0.1346112281990.06631572876080.1963145239980.01942092502840.02309236548270.3070151065220.03727510843720.3224503679212.966287845131.51657457917.6561288071
42.177899280090.963084027969-0.3312678263283.044854029480.7360515827640.7587104038660.05851915781390.271253478737-0.304162966072-0.211936010063-0.006028669273230.103797214670.00767472604969-0.0743474005526-0.00751009468860.2535276119890.00591567769669-0.02610511447880.226796035717-0.03094212829970.26726725775-0.277548697526-33.007937872127.8666288395
52.081782756340.0482209024348-0.7987074377641.07269908338-0.7535481810890.9754798082620.123090926315-0.01743338829880.00736732562825-0.09819171384480.1749181940320.1153597130190.2085808497080.123555070947-0.1143586046550.2978078663750.00506331930314-0.09066957682680.200774896974-0.03772617500130.3022881060413.7004813022-25.619528275928.415522757
61.726549196950.183574698351-1.172472978733.07258578346-0.2961756402083.466234476760.1749522834340.2343504045020.164426302148-0.138645267328-0.08762962185760.135085789138-0.194359339399-0.00410497813081-0.008493188131630.2810246886380.09202929112020.0198941584640.3415732238280.03725373062590.20786586056920.3979798023-20.834394740412.0877422527
71.66747184736-0.283979872581-0.9249649488852.576779245330.8057950992123.923606655080.07177699777970.00410800540196-0.223735840720.156361630875-0.132276566793-0.122599790530.2211810306090.238305336783-0.04008215885110.2046590955920.0162223701878-0.02928249516960.184347367809-0.001775948685940.28566434889312.3722561041-37.838468376830.6476351932
81.33619534874-0.457644026337-0.204412518490.742787368742-0.4769792908720.444944223510.0734566737016-0.2440297937070.4719824010050.01460047098710.027532326954-0.145556232445-0.1870803382490.0711457180356-0.005892545392080.303787929678-0.02224727023360.03375970550640.294696951455-0.07973118538980.4649340944691.92420231372-1.2522901966151.1599908243
91.29732108135-0.04377069016210.6296578533172.047618029940.1712044522651.278252589850.1393726697460.2583662716150.368891718595-0.5063993149470.277503800455-0.368312851742-0.302757261122-0.158925138781-0.05482159566470.47475604140.03074543235180.1993492423160.245751508780.08077136732320.501155869113-13.285149838410.84049528937.3035571178
100.0496992665512-0.19530733567-0.08112050514373.75056249718-0.01313393413280.978336911914-0.0310059341683-0.3665797175840.2568720637210.1320431027510.2338458949460.00731143030731-0.01250752572310.129959308294-0.05668296498430.249091455314-0.002589892750180.053941057470.317762842332-0.1055945217570.364518858857-6.42225597479-3.0436803031558.382020038
111.586845489160.163455230934-1.079658830640.9540044584021.022925779752.106189794070.0578956349971-0.07127046149390.0728631066442-0.0991438879495-0.02242554798370.007520911380370.06707321765150.0203690080349-0.04044425158720.2082802974230.0171271135661-0.007387267868250.227841632651-0.01236864236170.301077227815-26.44454412317.30650672594.59125223709
122.872306527710.271987868069-0.2416327937052.00901143129-0.1731610180512.02287487781-0.0482774490520.1039131187230.0707758483675-0.502374257606-0.1564457302320.0613801873503-0.1935844692960.0443885260811-0.04089100033290.3054347771550.027579988771-0.00697531028990.236440756417-0.004776310634590.226822496829-19.734986903518.0603247728-9.43333560445
133.535378379170.963228507751-0.1742105988291.195178876640.06188398221730.01789746903530.04421749984980.0160894727294-0.1272696242330.0412943738202-0.05982797972090.05874415082570.0556779375542-0.0272419541725-0.02866198060830.348209776801-0.03566509161550.00906435015220.260395379898-0.003059625237510.205150130356-22.2790082549-0.499622704587-5.55444021392
141.33178008897-0.1005622704-1.080278934020.2387055948540.4454019931171.42474489909-0.01781615705110.26876978332-0.345630998753-0.0564060162722-0.1028547829730.1078940515590.0791652409814-0.2785414791510.1619394015280.246260781749-0.00958620708278-0.01203015305860.285948685564-0.04170965909330.222962826636-31.7567983613-7.15321521289-11.7975219484
152.095332199911.01670037750.1364039832681.68128154869-0.9861998678541.416157774280.154728118283-0.09923220008870.1582694694760.198097577628-0.03529214118-0.147703161823-0.0237301747457-0.0279864932397-0.06581270496490.1938997794370.02811257650940.08777747404530.230274685195-0.05477572968240.215027064231-18.83113485936.691501023776.36929959923
161.96590718626-0.101931817391.131644050950.8816254960720.8168785362731.495128871370.1306790569340.0670001386112-0.2717334965820.0901913237395-0.04024330482770.02955127578430.0885896980824-0.2015857436690.003429513145530.224345938636-0.01554326937130.01558048574060.206429959149-0.009499938009570.261642661939-27.0949748101-24.398973118543.8587681903
171.8557855205-0.226507815978-0.4057907206673.26345274461-0.5672334746042.738272973880.0292559331397-0.2499380268270.03772627463220.2222271149630.003014891558550.1537845334680.371786881647-0.266053550960.103394665650.238908623034-0.03832839092540.04132186155430.2875949505160.02370192442820.221434525337-19.847709989-25.841391240557.4927573845
183.80529679461-1.93443255845-0.09673410615062.765736212730.1652261977770.752333705252-0.00731948671555-0.04709825769480.4200829172650.3213772684060.01084506040690.001619298767510.0203616176979-0.0706983860680.0367784583820.270737647034-0.009721670793330.05297954732360.252919718894-0.02901452409350.251552121763-22.5056502865-7.2061537911454.5254698918
191.624246777790.06985502455131.271478653240.6252020472891.240443615083.18632596079-0.0391525123509-0.03207692120450.1050695346990.0187021650417-0.1942299376340.0831584231532-0.0296005947651-0.05925198785450.1108282609530.195934861662-0.00976919639540.01226993878570.204498474240.01175657246390.203327735218-31.8929600381-1.03441948661.2805562487
204.34800988025-1.6899615278-0.6885636404010.703482429680.5921217118022.010612578320.3674552640370.2205502505150.00793655851359-0.0989276262141-0.226378457681-0.0067360596804-0.1340029467490.0147491747744-0.03116389646550.23289560563-0.0264595603605-0.001574896923190.1571108944160.0192428704620.230922946694-19.2763508927-13.683970534942.0628705105
211.353275672860.55318422514-0.9318852371111.800627152340.2511011928221.74859112172-0.09879257966340.0140748918821-0.03417352789020.04210237273590.191805054568-0.2936251212550.2531033233820.190777137469-0.007277214329340.2430767865260.0639729318415-0.004236241911270.277660174826-0.0443121875140.1996506035826.53005687861-8.26667241057-8.18285893301
221.80357381955-0.4417889096630.5728366065886.70054143837-0.9076391823421.480529222250.239893535262-0.3412996472080.3997525932420.0208778306623-0.3019344682410.2526170537420.03366896511250.6314192707080.4844032308140.239342463142-0.07900141865170.04465995410.408912508943-0.0594974046390.3071396820779.019849997411.353531055448.63335029365
230.409473032282-0.0073912453885-0.2104473761811.44560038093-0.1816045568590.189917867483-0.0955283874725-0.2274241206690.2357133102130.1249104547570.1892365698070.3013987121930.09237374323980.0537229719573-0.081828452430.2773297865420.0713733897342-0.02093547954660.357752387302-0.04888293038430.273621631917-5.89145921527-5.216180081252.74990482062
240.31783026699-0.3192902376460.1954883692582.33531218649-0.08886273482713.31102413501-0.172154476855-0.0278665696110.09594648895320.3798556221390.214469597637-0.0301285439170.2515488523210.07893528800110.0001521311125380.4176562532640.07182586801140.01429784784480.3487749818050.01916539144590.332785952691-12.6430696033-16.444126093112.8524439418
251.153976508831.32165372705-0.9429295670454.21708871161-0.8855440035870.9191473844790.02521098963780.05215454745190.125043846448-0.2268131058940.0914339075585-0.1423730318360.0113000825650.0536548926717-0.08260599674770.214875362140.00469043719037-0.02964055263370.201332853951-0.01768181388750.158413138612-6.09594858554-4.54048579429-9.38409536286
261.430102538021.619908344360.02432792995391.88198275827-0.4690181909961.374505742120.215845105616-0.219584557271-0.006636819277270.156324961439-0.034974101143-0.1739208316240.1023043195910.0458635692606-0.03342041865120.2360695131070.0127726358972-0.03102321437440.319956463254-0.05071816471870.259077888830.9407373103-22.997942746649.6416566984
271.209560282370.946284650581-0.7261074812811.20696296625-0.8142354202491.100460695350.394118683002-0.0117014719673-0.02256166034250.08826038765270.1608262805950.0893238965580.1819202753070.3768819128781.43775205960.304903355330.0623003248429-0.1080055855550.377303785291-0.1393724153410.27066724012528.417777421-33.599398770633.925489483
281.488015844760.140840714576-0.4256135024171.59766077177-0.4797412439990.9502090407150.2513432201770.315475624733-0.5093845379880.105435311065-0.08702277144460.003498078451430.1419249131090.169307139535-0.1388096928060.3182841682570.106705231002-0.1082765238510.392648760029-0.1442334344050.48530891273937.8364008718-41.603574810329.6504460686
294.175322102930.272421963707-1.299266590911.69008083879-0.1496694176282.165693713820.3202660036520.108242419084-0.0599619746102-0.165335601289-0.1560300410890.0980461250791-0.2816456182360.187863076329-0.1653622527810.242350299790.01428428166980.02548085552580.22590600476-0.033622380520.2427648616925.7198789017-19.845861742136.8626124841
303.0943424425-1.05320769448-1.192634219211.83824999253-0.006556280569470.8460534145120.06909911004240.0332519213294-0.294342537248-0.183522944897-0.0757357239637-0.0349808724215-0.0943303494793-0.0836790464396-0.05860588632070.2505818242110.01138372848650.03522799386640.274466000506-0.044144655030.24494707411234.55659335739.463658278151.53024049481
311.841570088590.0630679417532-6.14500979221E-52.87080440241-0.1256890938471.117819704130.1471562543790.2944396983640.0441746032483-0.5326809224890.00711204987083-0.172599244235-0.238488322750.0709716459893-0.08949571215240.3459960940890.0472625883080.03350659392280.3955316261270.03160668018210.26233984371128.144951657422.8386560569-4.42094789844
323.385495355170.3019687844270.5121329271140.457409270924-0.589469568690.961502403363-0.0834943811091-0.4081972332280.1685488225610.0547097526208-0.0459520044732-0.0432539466155-0.140984402479-0.4046464877940.09337155412850.2569438672750.03142964861430.03578813036740.238100201409-0.02256467915630.21947487421528.871706695226.842749764514.2029707411
332.62115338994-1.862122882770.3787291087754.108799967460.06038714699010.4154034491430.101770426814-0.1658798328740.185490429457-0.0524804554094-0.0187910559785-0.264040452664-0.111495401688-0.017123583379-0.06739132275790.24576195472-0.006718015308440.05890931928090.2945007321670.006072530607460.23913370301338.42979883834.824125711718.4657081017
345.011577338130.7862778133161.455533746511.819786126230.06944453118960.4241187935040.1814212879980.0984674968182-0.2348168273670.0025199455877-0.142692469327-0.0348202913470.2217823081360.0345162110268-0.09554228601250.2790112028980.005071608873260.03269591546510.279633635863-0.005966424401040.20230024291126.151646619713.178959577311.2533889104
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 123 )
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 217 )
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 263 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 93 )
5X-RAY DIFFRACTION5chain 'B' and (resid 94 through 116 )
6X-RAY DIFFRACTION6chain 'B' and (resid 117 through 217 )
7X-RAY DIFFRACTION7chain 'B' and (resid 218 through 261 )
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 123 )
9X-RAY DIFFRACTION9chain 'C' and (resid 124 through 217 )
10X-RAY DIFFRACTION10chain 'C' and (resid 218 through 262 )
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 65 )
12X-RAY DIFFRACTION12chain 'D' and (resid 66 through 93 )
13X-RAY DIFFRACTION13chain 'D' and (resid 94 through 123 )
14X-RAY DIFFRACTION14chain 'D' and (resid 124 through 217 )
15X-RAY DIFFRACTION15chain 'D' and (resid 218 through 261 )
16X-RAY DIFFRACTION16chain 'E' and (resid 4 through 65 )
17X-RAY DIFFRACTION17chain 'E' and (resid 66 through 93 )
18X-RAY DIFFRACTION18chain 'E' and (resid 94 through 123 )
19X-RAY DIFFRACTION19chain 'E' and (resid 124 through 217 )
20X-RAY DIFFRACTION20chain 'E' and (resid 218 through 261 )
21X-RAY DIFFRACTION21chain 'F' and (resid 4 through 65 )
22X-RAY DIFFRACTION22chain 'F' and (resid 66 through 79 )
23X-RAY DIFFRACTION23chain 'F' and (resid 80 through 123 )
24X-RAY DIFFRACTION24chain 'F' and (resid 124 through 217 )
25X-RAY DIFFRACTION25chain 'F' and (resid 218 through 261 )
26X-RAY DIFFRACTION26chain 'G' and (resid 4 through 93 )
27X-RAY DIFFRACTION27chain 'G' and (resid 94 through 123 )
28X-RAY DIFFRACTION28chain 'G' and (resid 124 through 217 )
29X-RAY DIFFRACTION29chain 'G' and (resid 218 through 263 )
30X-RAY DIFFRACTION30chain 'H' and (resid 4 through 47 )
31X-RAY DIFFRACTION31chain 'H' and (resid 48 through 93 )
32X-RAY DIFFRACTION32chain 'H' and (resid 94 through 123 )
33X-RAY DIFFRACTION33chain 'H' and (resid 124 through 217 )
34X-RAY DIFFRACTION34chain 'H' and (resid 218 through 263 )

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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