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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 4kfq | ||||||
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タイトル | Crystal structure of the NMDA receptor GluN1 ligand binding domain in complex with 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one | ||||||
![]() | Glutamate receptor ionotropic, NMDA 1 | ||||||
![]() | MEMBRANE PROTEIN / ligand binding domain / Ionotropic Glutamate Receptor | ||||||
機能・相同性 | ![]() pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane ...pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / voltage-gated monoatomic cation channel activity / regulation of monoatomic cation transmembrane transport / response to morphine / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / neuromuscular process / positive regulation of reactive oxygen species biosynthetic process / regulation of synapse assembly / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / regulation of axonogenesis / male mating behavior / suckling behavior / startle response / response to amine / monoatomic cation transmembrane transport / monoatomic cation transport / regulation of neuronal synaptic plasticity / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / ligand-gated monoatomic ion channel activity / cellular response to glycine / excitatory synapse / positive regulation of dendritic spine maintenance / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / cellular response to manganese ion / calcium ion homeostasis / glutamate receptor binding / prepulse inhibition / monoatomic cation channel activity / long-term memory / regulation of neuron apoptotic process / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / learning / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / calcium channel activity / visual learning / regulation of synaptic plasticity / response to organic cyclic compound / terminal bouton / cerebral cortex development / memory / synaptic vesicle membrane / intracellular calcium ion homeostasis / response to calcium ion / neuron cellular homeostasis / calcium ion transport / rhythmic process / synaptic vesicle / presynaptic membrane / signaling receptor activity / amyloid-beta binding / protein-containing complex assembly / chemical synaptic transmission / postsynaptic membrane / response to ethanol / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / dendritic spine / postsynaptic density / learning or memory 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Steffensen, T.B. / Tabrizi, F.M. / Gajhede, M. / Kastrup, J.S. | ||||||
![]() | ![]() タイトル: Crystal structure and pharmacological characterization of a novel N-methyl-D-aspartate (NMDA) receptor antagonist at the GluN1 glycine binding site. 著者: Kvist, T. / Steffensen, T.B. / Greenwood, J.R. / Mehrzad Tabrizi, F. / Hansen, K.B. / Gajhede, M. / Pickering, D.S. / Traynelis, S.F. / Kastrup, J.S. / Brauner-Osborne, H. #1: ![]() タイトル: Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA RECEPTOR NR1 ligand-binding core 著者: Furukawa, H. / Gouaux, E. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 141.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 110.8 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 484.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 493.4 KB | 表示 | |
XML形式データ | ![]() | 28.5 KB | 表示 | |
CIF形式データ | ![]() | 40.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 1pbqS S: 精密化の開始モデル |
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類似構造データ |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 33340.031 Da / 分子数: 2 / 断片: UNP residues 394-554, 663-800 / 由来タイプ: 組換発現 詳細: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUN1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 153 AND 154 OF THE ...詳細: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUN1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 153 AND 154 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (394-554, 663-800) 由来: (組換発現) ![]() ![]() ![]() ![]() #2: 化合物 | #3: 化合物 | ChemComp-GOL / #4: 化合物 | ChemComp-SO4 / #5: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.83 Å3/Da / 溶媒含有率: 56.56 % |
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結晶化 | 温度: 279 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one was added as solid compound and the solution was gently shaken overnight. 0.3 M ammonium sulfate, 0.1 M HEPES, and 30 % PEG ...詳細: 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one was added as solid compound and the solution was gently shaken overnight. 0.3 M ammonium sulfate, 0.1 M HEPES, and 30 % PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2010年12月18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: 0.91841 Å / 相対比: 1 |
反射 | 解像度: 2.2→39.69 Å / Num. all: 37896 / Num. obs: 37846 / % possible obs: 99.9 % / 冗長度: 3.2 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 7.1 |
反射 シェル | 解像度: 2.2→2.32 Å / 冗長度: 3.2 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5498 / Rsym value: 0.392 / % possible all: 100 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB entry 1PBQ 解像度: 2.2→39.69 Å / SU ML: 0.62 / Isotropic thermal model: Restrained / 交差検証法: THROUGHOUT / σ(F): 1.38 / 位相誤差: 21.78 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.86 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 48.896 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 27 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.2→39.69 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION
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