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- PDB-8chm: Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophen... -

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Basic information

Entry
Database: PDB / ID: 8chm
TitleHuman FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / FKBP12 / Inhibitor
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding / signaling receptor inhibitor activity / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / : / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / channel regulator activity / protein peptidyl-prolyl isomerization / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / peptidyl-prolyl cis-trans isomerase activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / T cell activation / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / negative regulation of transforming growth factor beta receptor signaling pathway / calcium ion transmembrane transport / Z disc / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein folding / regulation of protein localization / protein refolding / positive regulation of canonical NF-kappaB signal transduction / amyloid fibril formation / transmembrane transporter binding / Potential therapeutics for SARS / membrane / cytosol / cytoplasm
Similarity search - Function
: / 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
Similarity search - Domain/homology
: / Chem-UT6 / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsMeyners, C. / Purder, P.L. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Jacs Au / Year: 2023
Title: Deconstructing Protein Binding of Sulfonamides and Sulfonamide Analogues.
Authors: Purder, P.L. / Meyners, C. / Sugiarto, W.O. / Kolos, J. / Lohr, F. / Gebel, J. / Nehls, T. / Dotsch, V. / Lermyte, F. / Hausch, F.
History
DepositionFeb 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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 FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,90912
Polymers11,8321
Non-polymers1,07611
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.592, 40.081, 91.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding ...PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 11832.496 Da / Num. of mol.: 1 / Mutation: C22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62942, peptidylprolyl isomerase

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Non-polymers , 6 types, 225 molecules

#2: Chemical ChemComp-UT6 / (1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfinyl-5-ethenyl-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one


Mass: 464.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23Cl2N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.1 M ammonium sulfate, 0.2 M cadmium chloride, 0.1M HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.12→45.648 Å / Num. obs: 50936 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.015 / Rrim(I) all: 0.03 / Net I/σ(I): 30.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.13-45.616.10.0293820.9990.0170.034
1.12-1.147.20.09624760.9960.0560.111

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→45.648 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.556 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1455 2537 4.988 %
Rwork0.13 48329 -
all0.131 --
obs-50866 99.626 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.321 Å2
Baniso -1Baniso -2Baniso -3
1-1.555 Å20 Å20 Å2
2---0.7 Å2-0 Å2
3----0.855 Å2
Refinement stepCycle: LAST / Resolution: 1.12→45.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 47 214 1075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.012898
X-RAY DIFFRACTIONr_bond_other_d0.0060.016824
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.7071225
X-RAY DIFFRACTIONr_angle_other_deg0.8641.6191901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.00656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30610137
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.1611036
X-RAY DIFFRACTIONr_chiral_restr0.1650.2133
X-RAY DIFFRACTIONr_chiral_restr_other2.2310.25
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
X-RAY DIFFRACTIONr_nbd_refined0.2350.2145
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.2753
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2435
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2750.2133
X-RAY DIFFRACTIONr_metal_ion_refined0.1540.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.25
X-RAY DIFFRACTIONr_nbd_other0.1760.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3350.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0990.21
X-RAY DIFFRACTIONr_mcbond_it0.6870.971445
X-RAY DIFFRACTIONr_mcbond_other0.6870.971444
X-RAY DIFFRACTIONr_mcangle_it0.8731.755558
X-RAY DIFFRACTIONr_mcangle_other0.8721.754559
X-RAY DIFFRACTIONr_scbond_it1.3371.171453
X-RAY DIFFRACTIONr_scbond_other1.3291.169450
X-RAY DIFFRACTIONr_scangle_it1.6592.053667
X-RAY DIFFRACTIONr_scangle_other1.6452.045662
X-RAY DIFFRACTIONr_lrange_it2.80814.6811080
X-RAY DIFFRACTIONr_lrange_other2.10711.038978
X-RAY DIFFRACTIONr_rigid_bond_restr5.01131722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.12-1.1490.1181800.135200.10137300.9890.99399.19570.09
1.149-1.1810.1091730.09634090.09736070.9920.99499.30690.088
1.181-1.2150.1211710.09433600.09535510.9910.99499.43680.086
1.215-1.2520.1151840.09232090.09334120.9910.99599.44310.086
1.252-1.2930.1141520.09231590.09333320.9920.99599.36970.087
1.293-1.3390.1161530.09230680.09332250.9930.99599.8760.088
1.339-1.3890.1161590.09629400.09731040.9930.99499.83890.093
1.389-1.4460.1091520.09328420.09430080.9940.99599.53460.093
1.446-1.510.1141400.09627390.09628850.9920.99499.7920.099
1.51-1.5830.1071450.09826180.09927660.9930.99499.89150.103
1.583-1.6690.1191430.10224850.10326350.9910.99399.73430.113
1.669-1.770.1121180.10623620.10724830.9920.99399.87920.12
1.77-1.8920.1361100.11822490.11923650.9890.99199.74630.138
1.892-2.0430.121030.12621020.12522090.9910.99199.81890.151
2.043-2.2380.1591110.13419260.13520410.9850.98999.8040.164
2.238-2.5010.151990.14417460.14418470.9840.98799.89170.184
2.501-2.8870.17820.15915520.1616390.9810.98499.69490.207
2.887-3.5320.224640.17813550.1814240.9660.9899.64890.23
3.532-4.980.176660.15510520.15611210.9810.98599.73240.209
4.98-45.6480.193320.2146360.2136730.9840.96899.25710.324

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