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- PDB-4drn: EVALUATION OF SYNTHETIC FK506 ANALOGS AS LIGANDS FOR FKBP51 AND F... -

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Basic information

Entry
Database: PDB / ID: 4drn
TitleEVALUATION OF SYNTHETIC FK506 ANALOGS AS LIGANDS FOR FKBP51 AND FKBP52: COMPLEX OF FKBP51 WITH {3-[(1R)-3-(3,4-dimethoxyphenyl)-1-({[(2S)-1-{[(1S,2R)-2-ethyl-1-hydroxycyclohexyl](oxo)acetyl}piperidin-2-yl]carbonyl}oxy)propyl]phenoxy}acetic acid
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / Fk-506 binding domain / Hsp90 cochaperone / immunophilin / peptidyl-prolyl isomerase
Function / homology
Function and homology information


response to alcohol / FK506 binding / 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 / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity ...response to alcohol / FK506 binding / 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 / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / response to bacterium / response to cocaine / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
: / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. ...: / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-0MC / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.069 Å
AuthorsGopalakrishnan, R. / Kozany, C. / Gaali, S. / Kress, C. / Hoogeland, B. / Bracher, A. / Hausch, F.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Evaluation of Synthetic FK506 Analogues as Ligands for the FK506-Binding Proteins 51 and 52.
Authors: Gopalakrishnan, R. / Kozany, C. / Gaali, S. / Kress, C. / Hoogeland, B. / Bracher, A. / Hausch, F.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6662
Polymers14,0261
Non-polymers6401
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.270, 52.537, 57.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / 51 kDa FKBP / FKBP-51 / 54 kDa progesterone receptor- ...PPIase FKBP5 / 51 kDa FK506-binding protein / 51 kDa FKBP / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase


Mass: 14026.077 Da / Num. of mol.: 1 / Fragment: UNP residues 16-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIG6, FKBP5, FKBP51 / Plasmid: pProEx-HtB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+ RIL / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-0MC / {3-[(1R)-3-(3,4-dimethoxyphenyl)-1-({[(2S)-1-{[(1S,2R)-2-ethyl-1-hydroxycyclohexyl](oxo)acetyl}piperidin-2-yl]carbonyl}oxy)propyl]phenoxy}acetic acid


Mass: 639.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H45NO10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 37.5 % PEG3350, 0.1 M NH4OAc, 0.1 M HEPES pH 7.5, 10 % DMSO, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.069→25.057 Å / Num. all: 62752 / Num. obs: 62752 / % possible obs: 95.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.05 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.07-1.133.70.5761.43196086860.57691.4
1.13-1.23.70.3222.43160184800.32293.9
1.2-1.283.70.223.62980679990.2294.6
1.28-1.383.70.1535.12789175310.15395.4
1.38-1.513.70.0997.72596970090.09996.1
1.51-1.693.70.06111.82353264090.06196.8
1.69-1.953.60.04162091557450.0497.6
1.95-2.393.60.0319.91780849110.0398.1
2.39-3.383.70.02325.21421538780.02398.7
3.38-25.0573.30.02128.3701221040.02193

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O5Q

3o5q


Resolution: 1.069→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1649 / WRfactor Rwork: 0.1517 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9093 / SU B: 0.849 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0291 / SU Rfree: 0.0289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1724 3141 5 %RANDOM
Rwork0.1548 ---
all0.1557 62690 --
obs0.1557 59549 94.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 39.86 Å2 / Biso mean: 13.5351 Å2 / Biso min: 6.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.069→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 46 284 1310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221102
X-RAY DIFFRACTIONr_bond_other_d0.0020.02775
X-RAY DIFFRACTIONr_angle_refined_deg1.62.0231490
X-RAY DIFFRACTIONr_angle_other_deg0.8563.0061858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.185137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.4652542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.71115195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.197153
X-RAY DIFFRACTIONr_chiral_restr0.0920.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021223
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02202
X-RAY DIFFRACTIONr_nbd_refined0.2330.2226
X-RAY DIFFRACTIONr_nbd_other0.2060.2808
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2561
X-RAY DIFFRACTIONr_nbtor_other0.0970.2539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2195
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.233
X-RAY DIFFRACTIONr_mcbond_it1.4161.5715
X-RAY DIFFRACTIONr_mcbond_other0.5431.5275
X-RAY DIFFRACTIONr_mcangle_it1.80221079
X-RAY DIFFRACTIONr_scbond_it2.563479
X-RAY DIFFRACTIONr_scangle_it3.3524.5411
X-RAY DIFFRACTIONr_rigid_bond_restr1.3832094
X-RAY DIFFRACTIONr_sphericity_free5.8663291
X-RAY DIFFRACTIONr_sphericity_bonded3.1231848
LS refinement shellResolution: 1.069→1.097 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 211 -
Rwork0.275 4094 -
all-4305 -
obs--89.08 %

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