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

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Basic information

Entry
Database: PDB / ID: 4drm
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


Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / : / MECP2 regulates neuronal receptors and channels / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / peptidylprolyl isomerase ...Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / : / MECP2 regulates neuronal receptors and channels / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / peptidylprolyl isomerase / response to bacterium / peptidyl-prolyl cis-trans isomerase activity / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily ...: / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / 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 / isomorphous apo structure / Resolution: 1.48 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
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.162, 55.272, 56.822
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.: 228 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
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: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.48→42.162 Å / Num. all: 22844 / Num. obs: 22844 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.31 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.48-1.563.40.4771.51072731870.47797.1
1.56-1.653.50.2732.71091231260.273100
1.65-1.773.50.1774.11033529320.177100
1.77-1.913.50.1066.9974227540.106100
1.91-2.093.50.0729.5899025370.072100
2.09-2.343.50.05911.5820323110.059100
2.34-2.73.50.05311.7718820420.053100
2.7-3.33.50.04712.4616717610.047100
3.3-4.673.40.04114.3477613910.04199.9
4.67-42.1623.20.04111.725358030.04198.9

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Processing

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

3o5q


Resolution: 1.48→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2039 / WRfactor Rwork: 0.1749 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8961 / SU B: 2.631 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0746 / SU Rfree: 0.0769 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 1135 5 %RANDOM
Rwork0.176 ---
all0.1776 22738 --
obs0.1776 21603 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.58 Å2 / Biso mean: 12.8491 Å2 / Biso min: 4.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.48→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 46 228 1252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221100
X-RAY DIFFRACTIONr_angle_refined_deg1.6042.0291489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6915139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7492540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88115196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.721153
X-RAY DIFFRACTIONr_chiral_restr0.0970.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021832
X-RAY DIFFRACTIONr_mcbond_it0.811.5674
X-RAY DIFFRACTIONr_mcangle_it1.45321090
X-RAY DIFFRACTIONr_scbond_it2.4773426
X-RAY DIFFRACTIONr_scangle_it3.9614.5399
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.471 83 -
Rwork0.396 1555 -
all-1638 -
obs--99.27 %
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)
10.3789-0.13850.02170.53290.00080.3070.01020.0239-0.0216-0.01370.01140.0222-0.00470.0251-0.02160.00730.00170.00090.01860.00150.004530.004715.3749-9.6526
28.0737-0.5969-4.94060.2799-0.22313.40170.10310.3429-0.1068-0.1122-0.13920.02090.0617-0.07570.03610.05330.0115-0.01060.0642-0.00460.018932.830112.1577-19.7162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 139
2X-RAY DIFFRACTION2A201

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