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- PDB-7apt: The Fk1 domain of FKBP51 in complex with ((1S,5S,6R)-10-((3,5-dic... -

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Basic information

Entry
Database: PDB / ID: 7apt
TitleThe Fk1 domain of FKBP51 in complex with ((1S,5S,6R)-10-((3,5-dichlorophenyl)sulfonyl)-2-oxo-5-vinyl-3,10-diazabicyclo[4.3.1]decan-3-yl)acetic acid
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / conformation analysis / density functional calculations / FKBPs / magic methyl
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
Tetratricopeptide repeat / : / 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 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
Similarity search - Domain/homology
Chem-RRZ / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.131 Å
AuthorsKolos, M.J. / Pomplun, S. / Riess, B. / Purder, P. / Voll, M.A. / Merz, S. / Bracher, A. / Meyners, C. / Krewald, V. / Hausch, F.
CitationJournal: Chem Sci / Year: 2021
Title: Picomolar FKBP inhibitors enabled by a single water-displacing methyl group in bicyclic [4.3.1] aza-amides.
Authors: Kolos, J.M. / Pomplun, S. / Jung, S. / Riess, B. / Purder, P.L. / Voll, A.M. / Merz, S. / Gnatzy, M. / Geiger, T.M. / Quist-Lokken, I. / Jatzlau, J. / Knaus, P. / Holien, T. / Bracher, A. / ...Authors: Kolos, J.M. / Pomplun, S. / Jung, S. / Riess, B. / Purder, P.L. / Voll, A.M. / Merz, S. / Gnatzy, M. / Geiger, T.M. / Quist-Lokken, I. / Jatzlau, J. / Knaus, P. / Holien, T. / Bracher, A. / Meyners, C. / Czodrowski, P. / Krewald, V. / Hausch, F.
History
DepositionOct 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,4732
Polymers14,0261
Non-polymers4471
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.920, 54.550, 56.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated ...PPIase FKBP5 / 51 kDa FK506-binding protein / 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 / Mutation: A19T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-RRZ / 2-[(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-ethenyl-2-oxidanylidene-3,10-diazabicyclo[4.3.1]decan-3-yl]ethanoic acid / ((1S,5S,6R)-10-((3,5-dichlorophenyl)sulfonyl)-2-oxo-5-vinyl-3,10-diazabicyclo[4.3.1]decan-3-yl)acetic acid


Mass: 447.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20Cl2N2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 38% PEG-3340, 0.2 M NH4-acetate and HEPES-NaOH, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.13→39.17 Å / Num. obs: 47582 / % possible obs: 97.2 % / Redundancy: 3.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.131-1.152.60.413565921360.7760.2990.5132.287.5
3.069-39.173.20.051800925330.9930.030.0618.996.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.465
Highest resolutionLowest resolution
Rotation39.17 Å1.49 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o5q

3o5q


Resolution: 1.131→28.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.796 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 2536 5.2 %RANDOM
Rwork0.1671 ---
obs0.1695 46374 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.02 Å2 / Biso mean: 19.058 Å2 / Biso min: 9.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å2-0 Å20 Å2
2--0.03 Å2-0 Å2
3----2.22 Å2
Refinement stepCycle: final / Resolution: 1.131→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 28 155 1159
Biso mean--20.15 30.98 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0131103
X-RAY DIFFRACTIONr_bond_other_d0.0070.0171070
X-RAY DIFFRACTIONr_angle_refined_deg2.21.651492
X-RAY DIFFRACTIONr_angle_other_deg1.6321.5992505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4015142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1823.63644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88315210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.822153
X-RAY DIFFRACTIONr_chiral_restr0.1250.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021244
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02226
X-RAY DIFFRACTIONr_rigid_bond_restr12.33532173
LS refinement shellResolution: 1.131→1.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 171 -
Rwork0.402 3386 -
all-3557 -
obs--100 %

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