- PDB-9ey4: The FK1 domain of FKBP51 in complex with (3S,11S)-12-((3,5-dichlo... -
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Basic information
Entry
Database: PDB / ID: 9ey4
Title
The FK1 domain of FKBP51 in complex with (3S,11S)-12-((3,5-dichlorophenyl)sulfonyl)-5-oxo-11-vinyldecahydro-1H-6,10-epiminopyrrolo[1,2-a]azonine-3-carboxamide
Components
Peptidyl-prolyl cis-trans isomerase FKBP5
Keywords
ISOMERASE / FKBP51 / Inhibitor / Complex
Function / homology
Function and homology information
FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding ...FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol Similarity search - Function
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→39.175 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.813 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.1686
2145
4.778 %
Rwork
0.1424
42744
-
all
0.144
-
-
obs
-
44889
98.482 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 14.223 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.73 Å2
0 Å2
-0 Å2
2-
-
-0.558 Å2
0 Å2
3-
-
-
-0.172 Å2
Refinement step
Cycle: LAST / Resolution: 1.16→39.175 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
955
0
30
216
1201
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.012
1016
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.016
952
X-RAY DIFFRACTION
r_angle_refined_deg
1.997
1.837
1380
X-RAY DIFFRACTION
r_angle_other_deg
0.692
1.755
2210
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.738
5
128
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
6.597
11
5
X-RAY DIFFRACTION
r_dihedral_angle_other_2_deg
0.684
5
4
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.892
10
166
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
16.674
10
38
X-RAY DIFFRACTION
r_chiral_restr
0.117
0.2
154
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
1167
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
215
X-RAY DIFFRACTION
r_nbd_refined
0.201
0.2
183
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.199
0.2
875
X-RAY DIFFRACTION
r_nbtor_refined
0.182
0.2
520
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.089
0.2
541
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.212
0.2
134
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.136
0.2
7
X-RAY DIFFRACTION
r_nbd_other
0.215
0.2
41
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.293
0.2
29
X-RAY DIFFRACTION
r_mcbond_it
4.048
1.131
512
X-RAY DIFFRACTION
r_mcbond_other
3.962
1.128
511
X-RAY DIFFRACTION
r_mcangle_it
5.777
2.038
640
X-RAY DIFFRACTION
r_mcangle_other
5.776
2.039
641
X-RAY DIFFRACTION
r_scbond_it
9.747
1.368
504
X-RAY DIFFRACTION
r_scbond_other
9.738
1.368
505
X-RAY DIFFRACTION
r_scangle_it
11.018
2.393
740
X-RAY DIFFRACTION
r_scangle_other
11.01
2.393
741
X-RAY DIFFRACTION
r_lrange_it
19.036
17.77
1233
X-RAY DIFFRACTION
r_lrange_other
16.209
13.251
1138
X-RAY DIFFRACTION
r_rigid_bond_restr
4.932
3
1968
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
1.16-1.19
0.142
155
0.137
3165
0.137
3358
0.99
0.992
98.8684
0.125
1.19-1.223
0.19
143
0.136
3033
0.138
3210
0.979
0.991
98.9408
0.125
1.223-1.258
0.174
146
0.126
2978
0.128
3152
0.982
0.992
99.1117
0.117
1.258-1.297
0.154
161
0.125
2869
0.127
3059
0.988
0.991
99.052
0.117
1.297-1.339
0.153
148
0.114
2800
0.116
2969
0.984
0.992
99.2927
0.108
1.339-1.386
0.143
140
0.11
2720
0.111
2874
0.989
0.993
99.5129
0.105
1.386-1.438
0.147
126
0.117
2652
0.118
2793
0.986
0.992
99.4629
0.113
1.438-1.497
0.137
125
0.106
2552
0.107
2683
0.989
0.994
99.7764
0.104
1.497-1.564
0.147
146
0.111
2443
0.113
2595
0.985
0.993
99.7688
0.112
1.564-1.64
0.149
96
0.113
2354
0.114
2452
0.985
0.993
99.9184
0.116
1.64-1.728
0.136
134
0.113
2186
0.114
2326
0.989
0.992
99.7421
0.119
1.728-1.833
0.153
109
0.122
2125
0.124
2240
0.986
0.991
99.7321
0.131
1.833-1.959
0.141
122
0.133
1980
0.134
2107
0.987
0.989
99.7627
0.146
1.959-2.116
0.18
69
0.14
1900
0.141
1976
0.982
0.989
99.6458
0.159
2.116-2.317
0.179
76
0.136
1532
0.138
1798
0.983
0.989
89.4327
0.159
2.317-2.589
0.194
67
0.15
1578
0.151
1646
0.975
0.986
99.9392
0.18
2.589-2.988
0.173
80
0.167
1390
0.167
1474
0.98
0.983
99.7286
0.209
2.988-3.654
0.2
56
0.163
1067
0.164
1260
0.976
0.983
89.127
0.206
3.654-5.145
0.213
24
0.16
844
0.162
999
0.973
0.985
86.8869
0.22
5.145-39.175
0.226
22
0.247
576
0.246
610
0.971
0.965
98.0328
0.416
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