+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4d32 | ||||||
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タイトル | Structure of rat neuronal nitric oxide synthase heme domain in complex with 3-(3-fluorophenyl)-N-2-(2-(5-methyl-1H-imidazol-1-yl) pyrimidin-4-yl)ethylpropan-1-amine | ||||||
要素 | NITRIC OXIDE SYNTHASE, BRAIN | ||||||
キーワード | OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / retrograde trans-synaptic signaling by nitric oxide / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / positive regulation of sodium ion transmembrane transport ...Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / retrograde trans-synaptic signaling by nitric oxide / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / positive regulation of sodium ion transmembrane transport / Ion homeostasis / nitric oxide metabolic process / postsynaptic specialization, intracellular component / response to nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / calyx of Held / negative regulation of calcium ion transport / behavioral response to cocaine / regulation of neurogenesis / negative regulation of serotonin uptake / response to vitamin E / nitric-oxide synthase (NADPH) / sodium channel regulator activity / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / nitric oxide mediated signal transduction / negative regulation of insulin secretion / nitric-oxide synthase activity / xenobiotic catabolic process / multicellular organismal response to stress / arginine catabolic process / NADPH binding / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / sarcoplasmic reticulum membrane / T-tubule / nitric oxide biosynthetic process / cellular response to epinephrine stimulus / negative regulation of blood pressure / photoreceptor inner segment / response to hormone / response to nutrient levels / sarcoplasmic reticulum / secretory granule / response to activity / positive regulation of long-term synaptic potentiation / cell periphery / establishment of localization in cell / female pregnancy / phosphoprotein binding / response to lead ion / response to nicotine / establishment of protein localization / potassium ion transport / caveola / response to organic cyclic compound / sarcolemma / cellular response to growth factor stimulus / response to peptide hormone / Z disc / cellular response to mechanical stimulus / response to estrogen / vasodilation / calcium-dependent protein binding / calcium ion transport / FMN binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / flavin adenine dinucleotide binding / ATPase binding / response to heat / scaffold protein binding / nuclear membrane / response to ethanol / negative regulation of neuron apoptotic process / transmembrane transporter binding / mitochondrial outer membrane / response to lipopolysaccharide / dendritic spine / postsynaptic density / cytoskeleton / response to hypoxia / calmodulin binding / membrane raft / negative regulation of cell population proliferation / glutamatergic synapse / dendrite / heme binding / synapse / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II 類似検索 - 分子機能 | ||||||
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: 2.103 Å | ||||||
データ登録者 | Li, H. / Poulos, T.L. | ||||||
引用 | ジャーナル: J.Med.Chem. / 年: 2015 タイトル: Novel 2,4-Disubstituted Pyrimidines as Potent, Selective, and Cell-Permeable Inhibitors of Neuronal Nitric Oxide Synthase. 著者: Mukherjee, P. / Li, H. / Sevrioukova, I. / Chreifi, G. / Martasek, P. / Roman, L.J. / Poulos, T.L. / Silverman, R.B. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 4d32.cif.gz | 359.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4d32.ent.gz | 292.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4d32.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 4d32_validation.pdf.gz | 1.6 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4d32_full_validation.pdf.gz | 1.6 MB | 表示 | |
XML形式データ | 4d32_validation.xml.gz | 36.5 KB | 表示 | |
CIF形式データ | 4d32_validation.cif.gz | 50.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/d3/4d32 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/4d32 | HTTPS FTP |
-関連構造データ
関連構造データ | 4d2yC 4d2zC 4d30C 4d31C 4d33C 4d34C 4d35C 4d36C 4d37C 4d38C 4d39C 4d3aC 4d3bC 4uchC 4v3uC 4v3vC 4v3wC 4v3xC 4v3yC 4v3zC C: 同じ文献を引用 (文献) |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
-タンパク質 , 1種, 2分子 AB
#1: タンパク質 | 分子量: 48812.527 Da / 分子数: 2 / 断片: HEME DOMAIN, RESIDUES 297-718 / 由来タイプ: 組換発現 / 由来: (組換発現) RATTUS NORVEGICUS (ドブネズミ) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P29476, nitric-oxide synthase (NADPH) |
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-非ポリマー , 6種, 357分子
#2: 化合物 | #3: 化合物 | #4: 化合物 | #5: 化合物 | #6: 化合物 | ChemComp-ZN / | #7: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.46 Å3/Da / 溶媒含有率: 50.1 % / 解説: RMERGE 3.619 RPIM 1.767 CC ONE HALF 0.413 |
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結晶化 | pH: 5.8 詳細: 20-24% PEG3350, 0.1M MES, 10% ETHYLENE GLYCOL, 140-200 MM AMMONIUM ACETATE, 5 MM GSH, 35UM SDS, pH 5.8 |
-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: シンクロトロン / サイト: SSRL / ビームライン: BL7-1 / 波長: 1.127 |
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2014年7月12日 / 詳細: MIRRORS |
放射 | モノクロメーター: GRAPHITE / 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: 1.127 Å / 相対比: 1 |
反射 | 解像度: 2.1→50 Å / Num. obs: 56167 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / 冗長度: 5 % / Biso Wilson estimate: 30.14 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.7 |
反射 シェル | 解像度: 2.1→2.2 Å / 冗長度: 4.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.6 / % possible all: 97 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: NONE 解像度: 2.103→38.573 Å / SU ML: 0.32 / σ(F): 1.88 / 位相誤差: 30.9 / 立体化学のターゲット値: ML 詳細: RESIDUES 339 TO 349 IN CHAIN A AND 339 TO 347 IN CHAIN B ARE DISORDERED.
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.103→38.573 Å
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拘束条件 |
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LS精密化 シェル |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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