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- PDB-8chi: Human FKBP12 in complex with (1S,5S,6R)-10-((S)-3,5-dichloro-N-me... -

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Basic information

Entry
Database: PDB / ID: 8chi
TitleHuman FKBP12 in complex with (1S,5S,6R)-10-((S)-3,5-dichloro-N-methylphenylsulfonimidoyl)-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 / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / terminal cisterna ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / regulation of amyloid precursor protein catabolic process / protein maturation by protein folding / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / regulation of immune response / protein peptidyl-prolyl isomerization / supramolecular fiber organization / heart morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / T cell activation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / protein folding / positive regulation of protein binding / protein refolding / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transmembrane transporter binding / amyloid fibril formation / 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-UMR / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)24,7305
Polymers23,6652
Non-polymers1,0653
Water4,558253
1
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3262
Polymers11,8321
Non-polymers4931
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)12,4043
Polymers11,8321
Non-polymers5722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.361, 69.361, 129.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
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

#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
#2: Chemical ChemComp-UMR / (1S,5S,6R)-10-[S-[3,5-bis(chloranyl)phenyl]-N-methyl-sulfonimidoyl]-5-ethenyl-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one


Mass: 493.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26Cl2N4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.4M Na/K tartrate, 0.2 M ammonium citrate, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→47.444 Å / Num. obs: 35735 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 1 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.032 / Rrim(I) all: 0.118 / Net I/σ(I): 22.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-47.417.10.0331410.0090.031
1.7-1.7327.21.77618540.7320.4881.842

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.444 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.819 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2144 1703 4.776 %
Rwork0.178 33953 -
all0.18 --
obs-35656 99.978 %
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: 21.329 Å2
Baniso -1Baniso -2Baniso -3
1--0.107 Å20 Å20 Å2
2---0.107 Å20 Å2
3---0.214 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 68 253 1949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121790
X-RAY DIFFRACTIONr_bond_other_d0.0050.0161666
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.7132438
X-RAY DIFFRACTIONr_angle_other_deg0.8241.6253839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2955222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.431513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51110279
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.5431073
X-RAY DIFFRACTIONr_chiral_restr0.1390.2263
X-RAY DIFFRACTIONr_chiral_restr_other1.9790.212
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022107
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02411
X-RAY DIFFRACTIONr_nbd_refined0.2220.2277
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21538
X-RAY DIFFRACTIONr_nbtor_refined0.180.2863
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2930
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2175
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0940.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.211
X-RAY DIFFRACTIONr_nbd_other0.190.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.229
X-RAY DIFFRACTIONr_mcbond_it2.1182.238885
X-RAY DIFFRACTIONr_mcbond_other2.1192.238884
X-RAY DIFFRACTIONr_mcangle_it2.9924.0151108
X-RAY DIFFRACTIONr_mcangle_other2.9914.0141109
X-RAY DIFFRACTIONr_scbond_it3.2862.494905
X-RAY DIFFRACTIONr_scbond_other3.2882.498906
X-RAY DIFFRACTIONr_scangle_it4.5894.4211330
X-RAY DIFFRACTIONr_scangle_other4.5874.4241331
X-RAY DIFFRACTIONr_lrange_it5.9129.1582027
X-RAY DIFFRACTIONr_lrange_other5.7826.0221950
X-RAY DIFFRACTIONr_ncsr_local_group_10.1370.053088
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.137250.05008
12AX-RAY DIFFRACTIONLocal ncs0.137250.05008
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
1.7-1.7440.2471150.23424660.23525810.9610.9621000.222
1.744-1.7920.2641110.21523920.21725030.9530.9681000.196
1.792-1.8440.2591080.20223570.20524650.9520.9721000.181
1.844-1.90.2361130.20622590.20823720.9680.9721000.18
1.9-1.9630.211140.18522290.18623430.9670.9771000.162
1.963-2.0310.2381180.18520980.18822160.9630.9771000.161
2.031-2.1080.2241120.17520650.17821770.9680.9791000.152
2.108-2.1940.2221040.17719840.17920880.9690.981000.154
2.194-2.2910.1841010.16119110.16220120.980.9831000.14
2.291-2.4030.21780.18318590.18419370.9710.9791000.16
2.403-2.5320.238870.18117390.18418260.9610.981000.158
2.532-2.6850.209820.18116680.18217500.9730.9791000.158
2.685-2.870.252760.18915740.19216500.9550.9761000.171
2.87-3.0990.183740.18414580.18415320.9750.9781000.171
3.099-3.3940.199630.17713740.17814370.9770.9821000.169
3.394-3.7920.232650.16812420.17113070.9680.9831000.166
3.792-4.3740.176610.14710950.14811560.9880.9871000.15
4.374-5.3450.17470.1479610.14810080.9850.9881000.157
5.345-7.5120.194420.1827590.1838010.9730.981000.186
7.512-47.4440.311320.2274630.2325010.9430.96698.80240.242

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