- PDB-8c1y: Small molecule stabilizer for 14-3-3/ChREBP (Cmd 30) -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 8c1y
Title
Small molecule stabilizer for 14-3-3/ChREBP (Cmd 30)
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
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.51 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.178 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.12 / 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
0.2228
1329
5 %
RANDOM
Rwork
0.1892
-
-
-
obs
0.19091
25322
98.7 %
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Solvent computation
Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 32.267 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.39 Å2
0 Å2
-0 Å2
2-
-
-0.71 Å2
0 Å2
3-
-
-
-0.68 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→45.51 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2027
0
25
107
2159
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.016
2084
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.016
1903
X-RAY DIFFRACTION
r_angle_refined_deg
0.857
1.824
2806
X-RAY DIFFRACTION
r_angle_other_deg
0.368
1.564
4440
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.488
5.299
268
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
6.729
5
1
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.146
10
388
X-RAY DIFFRACTION
r_chiral_restr
0.039
0.2
302
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
2376
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
408
X-RAY DIFFRACTION
r_mcbond_it
7.507
2.69
1014
X-RAY DIFFRACTION
r_mcbond_other
7.505
2.689
1014
X-RAY DIFFRACTION
r_mcangle_it
9.871
4.001
1264
X-RAY DIFFRACTION
r_mcangle_other
9.88
4.004
1265
X-RAY DIFFRACTION
r_scbond_it
11.377
3.235
1070
X-RAY DIFFRACTION
r_scbond_other
11.372
3.237
1071
X-RAY DIFFRACTION
r_scangle_other
13.435
4.549
1543
X-RAY DIFFRACTION
r_long_range_B_refined
14.424
40.96
2470
X-RAY DIFFRACTION
r_long_range_B_other
14.483
39.256
2443
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.342
88
-
Rwork
0.304
1837
-
obs
-
-
98.11 %
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
1.0235
-0.3647
0.506
1.0814
-0.4019
1.4063
-0.0448
-0.048
0.0072
0.0606
0.0127
-0.0519
-0.0465
0.0353
0.0321
0.0377
0.0078
0.0058
0.0161
-0.0014
0.0179
-23.59
-16.624
8.04
2
5.0198
-0.7848
-0.2032
4.7755
0.406
8.7104
0.1318
0.1005
0.6809
-0.1764
-0.3073
-0.6591
-0.6639
0.2869
0.1755
0.0941
0.0013
0.01
0.0366
0.0629
0.2621
-11.29
-8.867
10.828
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