- PDB-9r8c: CRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH... -
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基本情報
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データベース: PDB / ID: 9r8c
タイトル
CRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1 AND A SELECTIVE DARPIN
要素
DESIGNED ANKYRIN REPEAT PROTEIN 3H10
Serine/threonine-protein kinase PLK1
キーワード
TRANSFERASE / DESIGN ANKYRIN REPEAT PROTEIN / DARPIN / SMALL MOLECULE INHIBITOR / DRUG DESIGN / KINASE / SERINE/THREONINE-PROTEIN KINASE
機能・相同性
機能・相同性情報
positive regulation of mitotic nuclear envelope disassembly / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / Phosphorylation of Emi1 / homologous chromosome segregation / mitotic nuclear membrane disassembly ...positive regulation of mitotic nuclear envelope disassembly / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / Phosphorylation of Emi1 / homologous chromosome segregation / mitotic nuclear membrane disassembly / metaphase/anaphase transition of mitotic cell cycle / female meiosis chromosome segregation / synaptonemal complex / Phosphorylation of the APC/C / anaphase-promoting complex binding / astral microtubule organization / Golgi inheritance / outer kinetochore / mitotic cleavage furrow formation / microtubule bundle formation / mitotic chromosome condensation / double-strand break repair via alternative nonhomologous end joining / Polo-like kinase mediated events / regulation of mitotic spindle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of mitotic metaphase/anaphase transition / centrosome cycle / positive regulation of ubiquitin-dependent protein catabolic process / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / spindle midzone / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / mitotic cytokinesis / mitotic sister chromatid segregation / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / establishment of protein localization / centriole / RHO GTPases Activate Formins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / kinetochore / positive regulation of protein localization to nucleus / G2/M transition of mitotic cell cycle / spindle / centriolar satellite / spindle pole / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / midbody / microtubule binding / protein phosphorylation / protein kinase activity / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / negative regulation of apoptotic process / chromatin / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能
Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily 類似検索 - ドメイン・相同性
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: 1.037 Å / 相対比: 1
反射
解像度: 2.24→96.16 Å / Num. obs: 233157 / % possible obs: 97.9 % / 冗長度: 4.2 % / Biso Wilson estimate: 40.5 Å2 / Rrim(I) all: 0.084 / Net I/σ(I): 14.6
反射 シェル
解像度: 2.24→2.38 Å / 冗長度: 3.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 28100 / Rrim(I) all: 1.118 / % possible all: 90.7
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.8.0419
精密化
XDS
VERSIONJun30, 2023BUILT=20230630
データ削減
SCALA
データスケーリング
PHASER
1.3
位相決定
精密化
構造決定の手法: 分子置換 / 解像度: 2.243→48.128 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 13.941 / SU ML: 0.166 / 交差検証法: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.199 / 詳細: Hydrogens have been added in their riding positions
Rfactor
反射数
%反射
Rfree
0.236
2826
5.106 %
Rwork
0.1882
52521
-
all
0.191
-
-
obs
-
55347
98.06 %
溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT
原子変位パラメータ
Biso mean: 50.407 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.604 Å2
0 Å2
-0 Å2
2-
-
-0.436 Å2
0 Å2
3-
-
-
-0.168 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.243→48.128 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
6620
0
100
329
7049
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.012
6927
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.016
6740
X-RAY DIFFRACTION
r_angle_refined_deg
1.352
1.869
9385
X-RAY DIFFRACTION
r_angle_other_deg
0.505
1.787
15556
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.41
5
855
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
7.278
5
50
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.776
10
1219
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
14.088
10
310
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
1061
X-RAY DIFFRACTION
r_chiral_restr_other
0.032
0.2
28
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
8013
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1515
X-RAY DIFFRACTION
r_nbd_refined
0.215
0.2
1388
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.191
0.2
6223
X-RAY DIFFRACTION
r_nbtor_refined
0.179
0.2
3361
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.074
0.2
3569
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.148
0.2
291
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.296
0.2
10
X-RAY DIFFRACTION
r_nbd_other
0.185
0.2
45
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.213
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
4.876
2.825
3375
X-RAY DIFFRACTION
r_mcbond_other
4.876
2.825
3375
X-RAY DIFFRACTION
r_mcangle_it
6.796
7.589
4218
X-RAY DIFFRACTION
r_mcangle_other
6.802
7.59
4219
X-RAY DIFFRACTION
r_scbond_it
6.044
3.327
3552
X-RAY DIFFRACTION
r_scbond_other
6.044
3.329
3553
X-RAY DIFFRACTION
r_scangle_it
8.471
8.759
5158
X-RAY DIFFRACTION
r_scangle_other
8.47
8.761
5159
X-RAY DIFFRACTION
r_lrange_it
10.332
30.643
7633
X-RAY DIFFRACTION
r_lrange_other
10.339
30.4
7586
X-RAY DIFFRACTION
r_ncsr_local_group_1
0.125
0.05
9080
X-RAY DIFFRACTION
r_ncsr_local_group_2
0.093
0.05
4117
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Refine-ID
タイプ
Rms dev position (Å)
Weight position
1
1
A
X-RAY DIFFRACTION
Localncs
0.12532
0.05008
1
2
A
X-RAY DIFFRACTION
Localncs
0.12532
0.05008
2
3
A
X-RAY DIFFRACTION
Localncs
0.09255
0.0501
2
4
A
X-RAY DIFFRACTION
Localncs
0.09255
0.0501
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20