- PDB-8bwe: Small molecule stabilizer for 14-3-3/ChREBP (Cmd 43) -
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Basic information
Entry
Database: PDB / ID: 8bwe
Title
Small molecule stabilizer for 14-3-3/ChREBP (Cmd 43)
Components
14-3-3 protein sigma
Carbohydrate-responsive element-binding protein
Keywords
STRUCTURAL PROTEIN / 14-3-3 / ChREBP / stabilization
Function / homology
Function and homology information
regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / RNA polymerase II transcription regulator complex / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / DNA-binding transcription factor activity / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function
14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein Similarity search - Domain/homology
Resolution: 2→46.46 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.203 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26229
961
4.8 %
RANDOM
Rwork
0.22719
-
-
-
obs
0.22888
19166
81.17 %
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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: 21.262 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.15 Å2
-0 Å2
0 Å2
2-
-
0.85 Å2
-0 Å2
3-
-
-
1.3 Å2
Refinement step
Cycle: LAST / Resolution: 2→46.46 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2027
0
29
124
2180
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.016
2085
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.016
1902
X-RAY DIFFRACTION
r_angle_refined_deg
1.301
1.823
2808
X-RAY DIFFRACTION
r_angle_other_deg
0.515
1.564
4438
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.166
5.299
268
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
3.231
5
1
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.664
10
388
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
302
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2377
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
407
X-RAY DIFFRACTION
r_mcbond_it
1.526
1.787
1014
X-RAY DIFFRACTION
r_mcbond_other
1.526
1.787
1014
X-RAY DIFFRACTION
r_mcangle_it
2.536
2.67
1264
X-RAY DIFFRACTION
r_mcangle_other
2.535
2.671
1265
X-RAY DIFFRACTION
r_scbond_it
1.847
1.968
1071
X-RAY DIFFRACTION
r_scbond_other
1.846
1.969
1072
X-RAY DIFFRACTION
r_scangle_other
2.96
2.87
1545
X-RAY DIFFRACTION
r_long_range_B_refined
5.397
22.584
2441
X-RAY DIFFRACTION
r_long_range_B_other
5.384
22.34
2427
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.343
62
-
Rwork
0.307
1485
-
obs
-
-
85.14 %
Refinement TLS params.
Method: refined / Origin x: 22.972 Å / Origin y: 20.446 Å / Origin z: 21.944 Å
11
12
13
21
22
23
31
32
33
T
0.2003 Å2
0.0265 Å2
-0.0205 Å2
-
0.0212 Å2
-0.0123 Å2
-
-
0.0121 Å2
L
0.9054 °2
0.139 °2
0.2567 °2
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1.1933 °2
0.6113 °2
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-
1.5733 °2
S
-0.0273 Å °
0.0223 Å °
0.0006 Å °
-0.0423 Å °
-0.0535 Å °
0.0838 Å °
0.0142 Å °
-0.1165 Å °
0.0808 Å °
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
-4 - 231
2
X-RAY DIFFRACTION
1
B
117 - 134
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