- PDB-4bdd: 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: 4bdd
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 / INHIBITOR
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 / replicative senescence / mitotic spindle assembly / 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 / replicative senescence / 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 / G2/M DNA damage checkpoint / protein catabolic process / PML body / Regulation of TP53 Activity through Methylation / 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 / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / cell division / 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 / 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: 2.67→39.99 Å / Cor.coef. Fo:Fc: 0.9472 / Cor.coef. Fo:Fc free: 0.9399 / SU R Cruickshank DPI: 0.379 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.382 / SU Rfree Blow DPI: 0.243 / SU Rfree Cruickshank DPI: 0.245 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
0.2198
636
4.91 %
RANDOM
Rwork
0.1865
-
-
-
obs
0.188
12944
99.25 %
-
原子変位パラメータ
Biso mean: 70.91 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.5056 Å2
0 Å2
0 Å2
2-
-
1.5056 Å2
0 Å2
3-
-
-
-3.0113 Å2
Refine analyze
Luzzati coordinate error obs: 0.354 Å
精密化ステップ
サイクル: LAST / 解像度: 2.67→39.99 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2178
0
34
46
2258
拘束条件
Refine-ID
タイプ
Dev ideal
数
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.009
2251
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.1
3047
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
766
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
49
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
335
HARMONIC
5
X-RAY DIFFRACTION
t_it
2251
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.28
X-RAY DIFFRACTION
t_other_torsion
17.67
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
301
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
2590
SEMIHARMONIC
4
LS精密化 シェル
解像度: 2.67→2.88 Å / Total num. of bins used: 7
Rfactor
反射数
%反射
Rfree
0.2631
146
5.54 %
Rwork
0.2112
2490
-
all
0.214
2636
-
obs
-
-
99.25 %
精密化 TLS
手法: refined / Origin x: -25.4392 Å / Origin y: 29.5243 Å / Origin z: 10.0684 Å