+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1vr2 | ||||||
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タイトル | HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 (KDR) KINASE DOMAIN | ||||||
要素 | PROTEIN (VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR KINASE) | ||||||
キーワード | TRANSFERASE (転移酵素) / TYROSINE KINASE (プロテインチロシンキナーゼ) | ||||||
機能・相同性 | 機能・相同性情報 blood vessel endothelial cell differentiation / cellular response to hydrogen sulfide / regulation of bone development / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / regulation of hematopoietic progenitor cell differentiation / endothelium development / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / vascular endothelial growth factor receptor-2 signaling pathway ...blood vessel endothelial cell differentiation / cellular response to hydrogen sulfide / regulation of bone development / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / regulation of hematopoietic progenitor cell differentiation / endothelium development / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / endocardium development / vascular wound healing / vascular endothelial growth factor receptor activity / post-embryonic camera-type eye morphogenesis / endothelial cell differentiation / mesenchymal cell proliferation / positive regulation of vasculogenesis / lymph vessel development / positive regulation of BMP signaling pathway / surfactant homeostasis / epithelial cell maturation / cell migration involved in sprouting angiogenesis / anchoring junction / positive regulation of positive chemotaxis / vascular endothelial growth factor signaling pathway / embryonic hemopoiesis / positive regulation of mesenchymal cell proliferation / positive regulation of mitochondrial fission / positive regulation of mitochondrial depolarization / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / lung alveolus development / positive regulation of stem cell proliferation / positive regulation of nitric-oxide synthase biosynthetic process / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / regulation of MAPK cascade / semaphorin-plexin signaling pathway / positive regulation of macroautophagy / : / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / calcium ion homeostasis / 細胞分化 / 脈管形成 / Integrin cell surface interactions / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / negative regulation of endothelial cell apoptotic process / peptidyl-tyrosine autophosphorylation / ovarian follicle development / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / VEGFR2 mediated cell proliferation / epithelial cell proliferation / stem cell proliferation / Hsp90 protein binding / 受容体型チロシンキナーゼ / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of angiogenesis / 遊走 / integrin binding / 細胞結合 / regulation of cell shape / protein tyrosine kinase activity / 血管新生 / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / エンドソーム / エンドソーム / positive regulation of cell migration / cadherin binding / positive regulation of protein phosphorylation / 脂質ラフト / external side of plasma membrane / negative regulation of gene expression / positive regulation of cell population proliferation / negative regulation of apoptotic process / ゴルジ体 / 小胞体 / extracellular region / ATP binding / identical protein binding / 細胞核 / 細胞膜 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 2.4 Å | ||||||
データ登録者 | Mctigue, M. / Wickersham, J. / Pinko, C. / Showalter, R. / Parast, C. / Tempczyk-Russell, A. / Gehring, M. / Mroczkowski, B. / Kan, C. / Villafranca, J. / Appelt, K. | ||||||
引用 | ジャーナル: Structure Fold.Des. / 年: 1999 タイトル: Crystal structure of the kinase domain of human vascular endothelial growth factor receptor 2: a key enzyme in angiogenesis. 著者: McTigue, M.A. / Wickersham, J.A. / Pinko, C. / Showalter, R.E. / Parast, C.V. / Tempczyk-Russell, A. / Gehring, M.R. / Mroczkowski, B. / Kan, C.C. / Villafranca, J.E. / Appelt, K. | ||||||
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 | 1vr2.cif.gz | 70.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1vr2.ent.gz | 50.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1vr2.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/vr/1vr2 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/1vr2 | HTTPS FTP |
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-関連構造データ
関連構造データ | 1fgkS S: 精密化の開始モデル |
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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
#1: タンパク質 | 分子量: 36274.738 Da / 分子数: 1 / 断片: KINASE DOMAIN / 変異: E990V / 由来タイプ: 組換発現 詳細: PROTEIN WAS AUTOPHOSPHORYLATED AT RESIDUE 1059 PRIOR TO CRYSTALLIZATION. THIS PROTEIN CONSTRUCT CONTAINS THE KINASE DOMAIN WITH 50 RESIDUES (RESIDUES 940- 989) OF THE KINASE INSERT DOMAIN ...詳細: PROTEIN WAS AUTOPHOSPHORYLATED AT RESIDUE 1059 PRIOR TO CRYSTALLIZATION. THIS PROTEIN CONSTRUCT CONTAINS THE KINASE DOMAIN WITH 50 RESIDUES (RESIDUES 940- 989) OF THE KINASE INSERT DOMAIN DELETED. THE PROTEIN ALSO CONTAINS A GLUTAMIC ACID TO VALINE MUTATION AT RESIDUE 990. 由来: (組換発現) Homo sapiens (ヒト) / 組織: AORTA 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P35968, EC: 2.7.1.112 |
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#2: 水 | ChemComp-HOH / |
-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: 2.41 Å3/Da / 溶媒含有率: 49.01 % | ||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 7.2 / 詳細: pH 7.2 | ||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / 手法: 蒸気拡散法, ハンギングドロップ法詳細: drop consists of equal volume of protein and mother-liquor | ||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: 回転陽極 / タイプ: RIGAKU RU200 / 波長: 1.5418 |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE |
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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.2→15 Å / Num. obs: 17234 / % possible obs: 93 % / 冗長度: 3.9 % / Rsym value: 0.052 / Net I/σ(I): 23.6 |
反射 シェル | 解像度: 2.2→2.28 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.196 / % possible all: 81.5 |
反射 | *PLUS Rmerge(I) obs: 0.052 |
反射 シェル | *PLUS % possible obs: 81.5 % / Rmerge(I) obs: 0.196 |
-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: PDB ENTRY 1FGK 解像度: 2.4→8 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 1.1 / σ(F): 2 /
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原子変位パラメータ | Biso mean: 31.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.4→8 Å
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拘束条件 |
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.1 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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