- PDB-4bdh: Fragment-based screening identifies a new area for inhibitor bind... -
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基本情報
登録情報
データベース: PDB / ID: 4bdh
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
機能・相同性
機能・相同性情報
mitotic DNA damage checkpoint signaling / regulation of autophagosome assembly / 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 / mitotic spindle assembly / replicative senescence / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage ...mitotic DNA damage checkpoint signaling / regulation of autophagosome assembly / 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 / mitotic spindle assembly / replicative senescence / 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 / PML body / cellular response to gamma radiation / intrinsic apoptotic signaling pathway in response to DNA damage / G2/M transition of mitotic cell cycle / 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 / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / DNA damage response / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm 類似検索 - 分子機能
解像度: 2.7→30.07 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.9361 / SU R Cruickshank DPI: 0.385 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.397 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.258 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
0.225
618
4.92 %
RANDOM
Rwork
0.177
-
-
-
obs
0.1792
12558
99.49 %
-
原子変位パラメータ
Biso mean: 69.78 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.0775 Å2
0 Å2
0 Å2
2-
-
3.0775 Å2
0 Å2
3-
-
-
-6.155 Å2
Refine analyze
Luzzati coordinate error obs: 0.337 Å
精密化ステップ
サイクル: LAST / 解像度: 2.7→30.07 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2172
0
29
65
2266
拘束条件
Refine-ID
タイプ
Dev ideal
数
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
2240
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.14
3034
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
756
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
47
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
333
HARMONIC
5
X-RAY DIFFRACTION
t_it
2240
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.59
X-RAY DIFFRACTION
t_other_torsion
18.13
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
302
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
2586
SEMIHARMONIC
4
LS精密化 シェル
解像度: 2.7→2.96 Å / Total num. of bins used: 6
Rfactor
反射数
%反射
Rfree
0.2649
156
5.25 %
Rwork
0.1968
2814
-
all
0.2003
2970
-
obs
-
-
99.49 %
精密化 TLS
手法: refined / Origin x: -25.3622 Å / Origin y: 29.4495 Å / Origin z: 10.3832 Å