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- PDB-8chl: Human FKBP12 in complex with (1S,5S,6R)-9-((3,5-dichlorophenyl)su... -

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Basic information

Entry
Database: PDB / ID: 8chl
TitleHuman FKBP12 in complex with (1S,5S,6R)-9-((3,5-dichlorophenyl)sulfonyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,9-diazabicyclo[4.2.1]nonan-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 / transforming growth factor beta receptor binding / cytoplasmic side of membrane / 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 / transforming growth factor beta receptor binding / cytoplasmic side of membrane / 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 / regulation of amyloid precursor protein catabolic process / signaling receptor inhibitor activity / terminal cisterna / ryanodine receptor complex / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / protein maturation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / protein folding / regulation of protein localization / protein refolding / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / membrane / cytoplasm / cytosol
Similarity search - Function
: / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
: / Chem-USV / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,14719
Polymers23,6652
Non-polymers2,48217
Water3,603200
1
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,30912
Polymers11,8321
Non-polymers1,47711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8387
Polymers11,8321
Non-polymers1,0066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.582, 70.582, 84.263
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 107 / Label seq-ID: 1 - 107

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2 / 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, 217 molecules

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


Mass: 480.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23Cl2N3O3S / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.2 M ammonium sulfate, 0.2 M cadmium sulfate

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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: Dec 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→42.13 Å / Num. obs: 46787 / % possible obs: 99.8 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.039 / Rrim(I) all: 0.083 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.67-42.1310.10.0283070.9980.0130.031
1.4-1.423.61.51822770.3131.0521.862

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→35.316 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.525 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2128 2257 4.829 %
Rwork0.1876 44484 -
all0.189 --
obs-46741 99.772 %
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: 15.121 Å2
Baniso -1Baniso -2Baniso -3
1--0.011 Å2-0.006 Å2-0 Å2
2---0.011 Å20 Å2
3---0.036 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 112 200 1922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121793
X-RAY DIFFRACTIONr_bond_other_d0.0050.0161658
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.7082438
X-RAY DIFFRACTIONr_angle_other_deg0.8871.6183829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7075220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.44458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57510267
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.5831066
X-RAY DIFFRACTIONr_chiral_restr0.1550.2272
X-RAY DIFFRACTIONr_chiral_restr_other2.1920.210
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02384
X-RAY DIFFRACTIONr_nbd_refined0.2090.2300
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21545
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2879
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2153
X-RAY DIFFRACTIONr_metal_ion_refined0.0930.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.215
X-RAY DIFFRACTIONr_nbd_other0.1780.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3160.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.160.21
X-RAY DIFFRACTIONr_mcbond_it1.6981.377880
X-RAY DIFFRACTIONr_mcbond_other1.6981.378879
X-RAY DIFFRACTIONr_mcangle_it2.6732.4741100
X-RAY DIFFRACTIONr_mcangle_other2.6722.4731101
X-RAY DIFFRACTIONr_scbond_it2.5731.558913
X-RAY DIFFRACTIONr_scbond_other2.5391.536902
X-RAY DIFFRACTIONr_scangle_it3.6162.751338
X-RAY DIFFRACTIONr_scangle_other3.5682.7081321
X-RAY DIFFRACTIONr_lrange_it5.20718.0032019
X-RAY DIFFRACTIONr_lrange_other5.02116.1561951
X-RAY DIFFRACTIONr_ncsr_local_group_10.1220.053081
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.122240.05008
12AX-RAY DIFFRACTIONLocal ncs0.122240.05008
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
1.4-1.4360.3471720.31532410.31734860.9050.92397.90590.315
1.436-1.4760.3391700.30431470.30633320.9090.92799.54980.305
1.476-1.5180.2551640.26431090.26432770.9540.94899.87790.263
1.518-1.5650.2671640.2530320.25132040.9520.95799.75030.245
1.565-1.6160.2521410.22829220.22930660.9570.96599.90220.218
1.616-1.6730.2291300.20728290.20829600.9670.97199.96620.191
1.673-1.7360.231260.20127520.20328780.9660.9741000.181
1.736-1.8060.2041390.18626480.18727870.9720.9781000.164
1.806-1.8870.1891330.17425010.17526340.9760.9811000.155
1.887-1.9780.1771260.16224070.16325330.9810.9841000.146
1.978-2.0850.1621160.15423180.15424350.9830.98699.95890.141
2.085-2.2110.1911190.15921730.16122920.9770.9841000.147
2.211-2.3630.177970.15720510.15821480.9810.9851000.146
2.363-2.5510.196990.17119110.17220100.9760.9821000.16
2.551-2.7930.199720.18517660.18618380.9750.9791000.177
2.793-3.1210.218730.18815980.18916710.9690.9781000.185
3.121-3.5990.199910.16813960.1714870.9760.9831000.175
3.599-4.3960.198530.15712120.15812650.9770.9851000.171
4.396-6.170.224400.1879320.1889720.9730.981000.204
6.17-35.3160.26320.2345390.2365710.9440.9641000.256
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)
10.3652-0.22260.22360.156-0.06330.43970.0022-0.0085-0.022-0.00020.01070.0092-0.007-0.0121-0.01290.00260.0056-0.00460.018-0.00550.0125-10.0525-28.1388-1.6821
21.0087-0.28-0.29510.35610.19640.13790.0202-0.06820.05410.0236-0.0013-0.02460.01470.0176-0.01880.01880.0095-0.00180.0208-0.0080.007-16.735-38.327-20.6109
Refinement TLS groupSelection: ALL

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