cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / syntaxin-1 binding / calcium/calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / syntaxin-1 binding / calcium/calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / postsynaptic density / calmodulin binding / non-specific serine/threonine protein kinase / negative regulation of translation / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / GTP binding / apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 1.9→28.56 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.241 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22764
1077
5.1 %
RANDOM
Rwork
0.17004
-
-
-
obs
0.17289
19907
99.91 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 22.607 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.55 Å2
0 Å2
0 Å2
2-
-
0.34 Å2
0 Å2
3-
-
-
0.2 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→28.56 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2436
0
28
225
2689
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2531
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.683
1.981
3448
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.885
5
316
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.397
24.25
120
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.514
15
459
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.012
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.119
0.2
378
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1933
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.224
0.2
1219
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.307
0.2
1775
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.174
0.2
216
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.265
0.2
1
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.264
0.2
98
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.229
0.2
28
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
1.542
2
1562
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.371
3
2476
X-RAY DIFFRACTION
r_scbond_it
1.74
2
1105
X-RAY DIFFRACTION
r_scangle_it
2.639
3
971
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.9→1.95 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.284
70
-
Rwork
0.185
1469
-
obs
-
-
99.48 %
+
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