- PDB-3ls8: Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morphol... -
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Basic information
Entry
Database: PDB / ID: 3ls8
Title
Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol
Components
Phosphatidylinositol 3-kinase catalytic subunit type 3
Keywords
TRANSFERASE / ALPHA/BETA PROTEIN / PIK3C3 / Phosphatidylinositol 3-kinase catalytic subunit type 3 / Compound 15e / STRUCTURAL GENOMICS / SGC STOCKHOLM / STRUCTURAL GENOMICS CONSORTIUM / SGC / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / INHIBITOR / PHOSPHATIDYLINOSITOL
Function / homology
Function and homology information
Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity ...Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / protein targeting to lysosome / early endosome to late endosome transport / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / Macroautophagy / axoneme / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / autophagosome maturation / autophagosome assembly / autophagosome / PI3K Cascade / RHO GTPases Activate NADPH Oxidases / regulation of macroautophagy / cellular response to glucose starvation / regulation of cytokinesis / regulation of autophagy / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / autophagy / endocytosis / phagocytic vesicle membrane / late endosome / peroxisome / kinase activity / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / protein kinase activity / endosome / cell division / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function
Phosphatidylinositol3-kinasecatalyticsubunittype3 / PtdIns-3-kinase type 3 / PI3-kinase type 3 / PI3K type 3 / Phosphoinositide-3-kinase class 3 / ...PtdIns-3-kinase type 3 / PI3-kinase type 3 / PI3K type 3 / Phosphoinositide-3-kinase class 3 / Phosphatidylinositol 3-kinase p100 subunit
Mass: 70118.203 Da / Num. of mol.: 2 / Fragment: UNP Residues 268-879 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase
Resolution: 2.25→70.9 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.439 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2507
3491
5.1 %
RANDOM
Rwork
0.20862
-
-
-
obs
0.21078
64837
99.26 %
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all
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64837
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 29.677 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.91 Å2
0 Å2
0 Å2
2-
-
-0.63 Å2
0 Å2
3-
-
-
2.54 Å2
Refinement step
Cycle: LAST / Resolution: 2.25→70.9 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8713
0
54
260
9027
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
8951
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
6178
X-RAY DIFFRACTION
r_angle_refined_deg
1.068
1.987
12117
X-RAY DIFFRACTION
r_angle_other_deg
0.853
3.001
15095
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.885
5
1086
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.536
24.729
425
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.879
15
1668
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.025
15
52
X-RAY DIFFRACTION
r_chiral_restr
0.063
0.2
1352
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
9778
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1716
X-RAY DIFFRACTION
r_mcbond_it
0.376
1.5
5378
X-RAY DIFFRACTION
r_mcbond_other
0.076
1.5
2142
X-RAY DIFFRACTION
r_mcangle_it
0.737
2
8729
X-RAY DIFFRACTION
r_scbond_it
1.251
3
3573
X-RAY DIFFRACTION
r_scangle_it
2.046
4.5
3377
LS refinement shell
Resolution: 2.25→2.308 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.357
257
-
Rwork
0.297
4428
-
obs
-
4685
93.59 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
6.6392
-2.0588
-1.247
4.6843
-0.4067
4.9208
-0.3533
-0.2829
-0.5228
0.1215
0.1228
0.1055
0.2255
-0.2087
0.2306
0.1693
-0.0017
0.0874
0.1322
0.0431
0.1253
-34.4789
14.2327
1.8436
2
1.7947
0.5781
-1.2959
1.6054
-1.1536
3.4825
-0.0217
-0.1641
-0.1025
0.1823
-0.046
-0.1102
0.0427
0.1462
0.0677
0.0348
0.0104
-0.0245
0.1013
-0.0328
0.091
-10.9636
25.346
-19.9134
3
1.6369
0.2587
-0.5135
7.7922
-0.8674
3.0936
0.0075
0.1554
0.1466
-0.2957
0.0923
-0.4191
-0.1643
0.1298
-0.0998
0.0267
-0.0198
0.0191
0.1256
-0.0403
0.0897
-12.399
38.1405
-43.3727
4
1.9003
-0.1643
0.2978
0.4404
-0.552
1.629
0.0326
-0.0597
0.1187
-0.0006
0.038
0.1015
-0.1113
-0.1738
-0.0706
0.0286
0.0032
0.0253
0.0489
-0.024
0.097
-38.4765
35.391
-29.9197
5
12.2094
-2.6535
-0.2542
6.9225
1.5163
3.9659
-0.427
-2.233
0.0415
1.9405
0.6382
-0.5369
0.4276
0.3317
-0.2112
1.1677
0.1533
-0.1776
0.8765
-0.1224
0.312
-37.0501
86.6787
5.9411
6
2.7185
-0.3844
0.1335
3.8744
0.3502
5.5254
-0.0184
-0.3863
0.0583
0.8321
0.1289
-0.0314
-0.1917
-0.0373
-0.1106
0.3069
0.0419
0.0402
0.1318
0.0282
0.1143
-48.4871
83.2751
-15.0353
7
0.9984
-0.8981
-0.2251
2.1381
0.399
0.9967
0.1032
0.0855
0.0665
-0.1193
0.0019
-0.1686
-0.0118
-0.0647
-0.1051
0.1211
-0.019
0.0161
0.0597
0.055
0.1675
-38.2103
72.1675
-36.3346
8
2.9599
-0.8641
-1.0911
1.5706
0.5129
2.9184
-0.1181
-0.4086
-0.0568
0.5646
0.4293
-0.8308
0.3678
0.4588
-0.3112
0.3941
0.1129
-0.3054
0.2042
-0.2004
0.6042
-21.3815
70.7328
-17.6341
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
282 - 361
2
X-RAY DIFFRACTION
2
A
362 - 562
3
X-RAY DIFFRACTION
3
A
563 - 639
4
X-RAY DIFFRACTION
4
A
640 - 871
5
X-RAY DIFFRACTION
5
B
296 - 353
6
X-RAY DIFFRACTION
6
B
354 - 510
7
X-RAY DIFFRACTION
7
B
511 - 767
8
X-RAY DIFFRACTION
8
B
768 - 871
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