+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1kms | ||||||
---|---|---|---|---|---|---|---|
タイトル | HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 6-([5-QUINOLYLAMINO]METHYL)-2,4-DIAMINO-5-METHYLPYRIDO[2,3-D]PYRIMIDINE (SRI-9439), A LIPOPHILIC ANTIFOLATE | ||||||
要素 | DIHYDROFOLATE REDUCTASE | ||||||
キーワード | OXIDOREDUCTASE / ANTIPARASITIC DRUGS / REDUCTASE / LIPOPHILIC ANTIFOLATES | ||||||
機能・相同性 | 機能・相同性情報 regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.09 Å | ||||||
データ登録者 | Klon, A.E. / Heroux, A. / Ross, L.J. / Pathak, V. / Johnson, C.A. / Piper, J.R. / Borhani, D.W. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2002 タイトル: Atomic structures of human dihydrofolate reductase complexed with NADPH and two lipophilic antifolates at 1.09 a and 1.05 a resolution. 著者: Klon, A.E. / Heroux, A. / Ross, L.J. / Pathak, V. / Johnson, C.A. / Piper, J.R. / Borhani, D.W. | ||||||
履歴 |
|
-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
-ダウンロード
PDBx/mmCIF形式 | 1kms.cif.gz | 116.6 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1kms.ent.gz | 90.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1kms.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/km/1kms ftp://data.pdbj.org/pub/pdb/validation_reports/km/1kms | HTTPS FTP |
---|
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-要素
#1: タンパク質 | 分子量: 21349.525 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PDFR / 生物種 (発現宿主): Escherichia coli / 細胞内の位置 (発現宿主): CYTOPLASM / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P00374, dihydrofolate reductase | ||||||
---|---|---|---|---|---|---|---|
#2: 化合物 | #3: 化合物 | ChemComp-LIH / | #4: 化合物 | ChemComp-NDP / | #5: 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 |
---|
-試料調製
結晶 | マシュー密度: 2.23 Å3/Da / 溶媒含有率: 46 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 詳細: THE TERNARY COMPLEX OF DHFR WITH NADPH AND SRI-9439 WAS FORMED BY MIXING HUMAN DHFR (20 MG/ML IN 25 MM KPO4 (PH 7.0), 0.1 MM EDTA, AND 3 MM NAN3) WITH 60 MM NADPH, FOLLOWED 15 MINUTES LATER ...詳細: THE TERNARY COMPLEX OF DHFR WITH NADPH AND SRI-9439 WAS FORMED BY MIXING HUMAN DHFR (20 MG/ML IN 25 MM KPO4 (PH 7.0), 0.1 MM EDTA, AND 3 MM NAN3) WITH 60 MM NADPH, FOLLOWED 15 MINUTES LATER BY 60 MM OF INHIBITOR IN DMSO (FINAL CONCENTRATIONS OF 2 MM NADPH AND 2 MM INHIBITOR). THIS COMPLEX SOLUTION WAS MIXED WITH AN EQUAL VOLUME OF PRECIPITANT CONTAINING 24-33% PEG 4000, 0.2 M LI2SO4, 0.1 M TRIS CL (PH 7.9-8.4), AND EQUILIBRATED WITH THE PRECIPITANT BY HANGING DROP VAPOR DIFFUSION AT 277 K. THE CRYSTAL GREW IN ABOUT 3 WEEKS. THE CRYSTAL WAS FLASH-COOLED DIRECTLY IN LIQUID NITROGEN AFTER HARVESTING INTO MOTHER LIQUOR CONTAINING 10% GLYCEROL., pH 8.00, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
|
-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: SSRL / ビームライン: BL7-1 / 波長: 1.08 |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1997年6月25日 / 詳細: PT-COATED MIRROR |
放射 | モノクロメーター: SI (111) / 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: 1.08 Å / 相対比: 1 |
反射 | 解像度: 1.09→20 Å / Num. all: 79611 / Num. obs: 79611 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.6 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 9.4 |
反射 シェル | 解像度: 1.09→1.15 Å / 冗長度: 3.3 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.422 / % possible all: 99.1 |
反射 | *PLUS 最高解像度: 1.09 Å / 最低解像度: 20 Å / Num. measured all: 289350 / Rmerge(I) obs: 0.047 |
反射 シェル | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.422 |
-解析
ソフトウェア |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: 分子置換 開始モデル: UNPUBLISHED HUMAN DHFR STRUCTURE. 解像度: 1.09→20 Å / Num. parameters: 18984 / Num. restraintsaints: 23468 / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: ENGH & HUBER 詳細: REFINEMENT IN X-PLOR, ALTERNATED WITH MANUAL REBUILDING IN O, RESULTING IN A FREE R-FACTOR OF 24.0%. SRI-9439 WAS THEN ADDED TO THE MODEL IN THE ACTIVE SITE AND THE CIS PEPTIDE BONDS BETWEEN ...詳細: REFINEMENT IN X-PLOR, ALTERNATED WITH MANUAL REBUILDING IN O, RESULTING IN A FREE R-FACTOR OF 24.0%. SRI-9439 WAS THEN ADDED TO THE MODEL IN THE ACTIVE SITE AND THE CIS PEPTIDE BONDS BETWEEN RESIDUES ARG-65 AND PRO-66 AND RESIDUES GLY-116 AND GLY-117 BECAME APPARENT IN 2FO-FC AND FO-FC MAPS. REFINEMENT PROCEEDED WITH THE ADDITION OF RIDING HYDROGEN ATOMS AND ANISOTROPIC TEMPERATURE FACTORS IN REFMAC AND ARP, YIELDING A FREE R-FACTOR OF 19.4%. AT THIS POINT, MOST OF THE SIDE CHAIN ALTERNATE CONFORMATIONS WERE MODELED. ANISOTROPIC DISPLACEMENT PARAMETERS WERE REFINED IN SHELXL AND RIDING HYDROGEN ATOMS WERE ADDED. IN THE FINAL ROUNDS OF REFINEMENT, RESTRAINTS FOR ALL ATOMS IN SRI-9439 EXCEPT FOR PLANARITY RESTRAINTS ON THE 5-QUINOLYLAMINO GROUP, AND ALL NADPH ATOMS EXCEPT FOR THOSE IN THE ADENINE RING AND ADENINE RIBOSE-2-PHOSPHATE WERE REMOVED, GIVING THE FINAL FREE R-FACTOR (17.3%). ATTEMPTS TO RESTRAIN THE PLANARITY OF THE 5-METHYL-5-DEAZAPTERIDINE MOIETY OF SRI-9439 RESULTED IN LARGE DIFFERENCE ELECTRON DENSITY PEAKS FOR THE EXOCYCLIC N4 AND C5A ATOMS, CONFIRMING THEIR OUT-OF-PLANE POSITIONS.
| |||||||||||||||||||||||||||||||||
溶媒の処理 | 溶媒モデル: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 66 / Occupancy sum hydrogen: 1406.12 / Occupancy sum non hydrogen: 1927.22 | |||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.09→20 Å
| |||||||||||||||||||||||||||||||||
拘束条件 |
| |||||||||||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: SHELXL / バージョン: 97 / 分類: refinement | |||||||||||||||||||||||||||||||||
精密化 | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.173 / Rfactor Rwork: 0.131 | |||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
|