- PDB-3s3h: Crystal structure of the catalytic domain of PTP10D from Drosophi... -
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基本情報
登録情報
データベース: PDB / ID: 3s3h
タイトル
Crystal structure of the catalytic domain of PTP10D from Drosophila melanogaster with a phosphopeptide substrate GP4
要素
Tyrosine-protein phosphatase 10D
phosphopeptide GP4
キーワード
HYDROLASE (加水分解酵素) / Differentiation / Neurogenesis (神経発生) / Signal transduction (シグナル伝達) / developmental Protein (ヒトの発達) / Protein Phosphatase (プロテインホスファターゼ) / Protein Tyrosine Phosphatase (プロテインチロシンホスファターゼ)
機能・相同性
機能・相同性情報
branching involved in open tracheal system development / open tracheal system development / negative regulation of fibroblast growth factor receptor signaling pathway / Neutrophil degranulation / transmembrane receptor protein tyrosine phosphatase activity / motor neuron axon guidance / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / long-term memory / protein dephosphorylation ...branching involved in open tracheal system development / open tracheal system development / negative regulation of fibroblast growth factor receptor signaling pathway / Neutrophil degranulation / transmembrane receptor protein tyrosine phosphatase activity / motor neuron axon guidance / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / long-term memory / protein dephosphorylation / プロテインチロシンホスファターゼ / central nervous system development / protein tyrosine phosphatase activity / 軸索誘導 / apical part of cell / 神経繊維 / 生体膜 類似検索 - 分子機能
PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / フィブロネクチンIII型ドメイン / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta 類似検索 - ドメイン・相同性
解像度: 2.8→44.47 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.815 / SU B: 28.434 / SU ML: 0.266 / Isotropic thermal model: isotropic / 交差検証法: THROUGHOUT / ESU R Free: 0.359 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.289
1343
5 %
RANDOM
Rwork
0.25
-
-
-
obs
0.252
25293
99.9 %
-
all
-
25293
-
-
溶媒の処理
溶媒モデル: BABINET MODEL PARAMETERS FOR MASK CACLULATION
原子変位パラメータ
Biso mean: 49.61 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.11 Å2
0.05 Å2
0 Å2
2-
-
0.11 Å2
0 Å2
3-
-
-
-0.16 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.8→44.47 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
4691
0
11
82
4784
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
4841
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.401
1.928
6565
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.063
5
570
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.212
22.731
260
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.978
15
777
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.452
15
49
X-RAY DIFFRACTION
r_chiral_restr
0.101
0.2
681
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
3812
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
数: 2261 / タイプ: medium positional / Rms dev position: 0.63 Å / Weight position: 0.5