- PDB-4bdi: Fragment-based screening identifies a new area for inhibitor bind... -
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基本情報
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データベース: PDB / ID: 4bdi
タイトル
Fragment-based screening identifies a new area for inhibitor binding to checkpoint kinase 2 (CHK2)
要素
SERINE/THREONINE-PROTEIN KINASE CHK2
キーワード
TRANSFERASE (転移酵素)
機能・相同性
機能・相同性情報
mitotic DNA damage checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / ヘイフリック限界 / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...mitotic DNA damage checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / ヘイフリック限界 / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / protein catabolic process / G2/M DNA damage checkpoint / Regulation of TP53 Activity through Methylation / cellular response to gamma radiation / PML body / G2/M transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / Regulation of TP53 Degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / 細胞分裂 / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ubiquitin protein ligase binding / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / ゴルジ体 / protein homodimerization activity / 核質 / ATP binding / identical protein binding / metal ion binding / 細胞核 / 細胞質 類似検索 - 分子機能
解像度: 2.32→39.07 Å / Cor.coef. Fo:Fc: 0.9578 / Cor.coef. Fo:Fc free: 0.9407 / SU R Cruickshank DPI: 0.21 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.209 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.177 詳細: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
Rfactor
反射数
%反射
Selection details
Rfree
0.2205
989
5.12 %
RANDOM
Rwork
0.188
-
-
-
obs
0.1896
19304
99.73 %
-
原子変位パラメータ
Biso mean: 75.78 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.4699 Å2
0 Å2
0 Å2
2-
-
2.4699 Å2
0 Å2
3-
-
-
-4.9398 Å2
Refine analyze
Luzzati coordinate error obs: 0.341 Å
精密化ステップ
サイクル: LAST / 解像度: 2.32→39.07 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2225
0
52
53
2330
拘束条件
Refine-ID
タイプ
Dev ideal
数
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
2313
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.09
3124
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
787
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
50
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
340
HARMONIC
5
X-RAY DIFFRACTION
t_it
2313
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.57
X-RAY DIFFRACTION
t_other_torsion
16.48
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
308
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
2688
SEMIHARMONIC
4
LS精密化 シェル
解像度: 2.32→2.44 Å / Total num. of bins used: 10
Rfactor
反射数
%反射
Rfree
0.244
137
4.96 %
Rwork
0.2107
2627
-
all
0.2125
2764
-
obs
-
-
99.73 %
精密化 TLS
手法: refined / Origin x: -12.6538 Å / Origin y: 36.2432 Å / Origin z: 5.2338 Å