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- PDB-4drp: Evaluation of Synthetic FK506 Analogs as Ligands for the FK506-Bi... -

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Basic information

Entry
Database: PDB / ID: 4drp
TitleEvaluation of Synthetic FK506 Analogs as Ligands for the FK506-Binding Proteins 51 and 52: Complex of FKBP51 with 2-(3-((R)-3-(3,4-dimethoxyphenyl)-1-((S)-1-(2-((1R,2S)-2-ethyl-1-hydroxy-cyclohexyl)-2-oxoacetyl)piperidine-2-carbonyloxy)propyl)phenoxy)acetic acid from cocrystallization
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / Fk-506 binding domain / Hsp90 cochaperone / immunophilin / peptidyl-prolyl isomerase
Function / homology
Function and homology information


FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / 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 / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / 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 / 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-0MD / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.913, 56.563, 57.589
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-0MD / {3-[(1R)-3-(3,4-dimethoxyphenyl)-1-({[(2S)-1-{[(1R,2S)-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.: 173 / 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: 2.9 Å3/Da / Density % sol: 57.56 %
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: 1.792→25.386 Å / Num. all: 15448 / Num. obs: 15448 / % possible obs: 97.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.88 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.79-1.892.30.193.9433318620.1984
1.89-23.30.1882.8708721330.18899.6
2-2.143.50.1026.7710220290.102100
2.14-2.313.50.1073671319020.107100
2.31-2.533.50.0749.3618717550.074100
2.53-2.833.50.0659.8564515970.065100
2.83-3.273.50.05711.3501614290.057100
3.27-4.013.40.05610.2418312160.056100
4.01-5.673.30.04613.431989670.046100
5.67-25.3863.10.03415.817525580.03497.2

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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: PDB ENTRY 3O5Q

3o5q


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.2657 / WRfactor Rwork: 0.2229 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.831 / SU B: 6.567 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1426 / SU Rfree: 0.1384 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 769 5 %RANDOM
Rwork0.22 ---
all0.2221 14853 --
obs0.2221 14559 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.32 Å2 / Biso mean: 20.0242 Å2 / Biso min: 7.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 46 173 1205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221055
X-RAY DIFFRACTIONr_angle_refined_deg1.4722.031419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5475127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.482540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54315187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.585153
X-RAY DIFFRACTIONr_chiral_restr0.10.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021780
X-RAY DIFFRACTIONr_mcbond_it0.681.5638
X-RAY DIFFRACTIONr_mcangle_it1.16421025
X-RAY DIFFRACTIONr_scbond_it1.8763417
X-RAY DIFFRACTIONr_scangle_it2.9274.5394
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 37 -
Rwork0.227 869 -
all-906 -
obs--80.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.6930.21070.09030.8625-0.09060.8509-0.02560.0168-0.0015-0.03160.03170.02540.06150.0273-0.00610.01750.00350.00760.0454-0.00110.03421.415912.90136.302
24.4344-0.0763-0.52525.2802-2.78331.5396-0.2181-0.24050.1097-0.22010.1525-0.13130.1502-0.04780.06560.092-0.0220.02240.0652-0.01860.03661.14422.76711.1265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 140
2X-RAY DIFFRACTION2A201

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