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- PDB-9dcw: FKBP1a (FKBP12) co-crystal structure with macrocycle molecular glue -

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Basic information

Entry
Database: PDB / ID: 9dcw
TitleFKBP1a (FKBP12) co-crystal structure with macrocycle molecular glue
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsIMMUNOSUPPRESSANT / Molecular Glue
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 / 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 / calcium channel regulator activity / protein maturation / T cell activation / peptidyl-prolyl cis-trans isomerase activity / sarcoplasmic reticulum / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / 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 / cytosol / cytoplasm
Similarity search - Function
: / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
: / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.721 Å
AuthorsSalcius, M.J. / King, D.A. / Clark, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Identification and characterization of ternary complexes consisting of FKBP12, MAPRE1 and macrocyclic molecular glues.
Authors: Salcius, M. / Tutter, A. / Fouche, M. / Koc, H. / King, D. / Dhembi, A. / Golosov, A. / Jahnke, W. / Henry, C. / Argoti, D. / Jia, W. / Pedro, L. / Connor, L. / Piechon, P. / Fabbiani, F. / ...Authors: Salcius, M. / Tutter, A. / Fouche, M. / Koc, H. / King, D. / Dhembi, A. / Golosov, A. / Jahnke, W. / Henry, C. / Argoti, D. / Jia, W. / Pedro, L. / Connor, L. / Piechon, P. / Fabbiani, F. / Denay, R. / Sager, E. / Kuehnoel, J. / Lozach, M.A. / Lima, F. / Vitrey, A. / Chen, S.Y. / Michaud, G. / Roth, H.J.
History
DepositionAug 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8172
Polymers12,0551
Non-polymers7621
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.490, 62.984, 68.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+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: 12054.782 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Chemical ChemComp-A1AZI / (5S,14R,16aS,21R,28S,30aR)-14-[2-(3,4-dimethoxyphenyl)ethyl]-24,24,28-trimethyl-2-methylidene-1,3,4,17,18,19,20,24,25,28,29,30a-dodecahydro-2H,14H-9,13-(metheno)dipyrido[1,2-d:1',2'-o][1,10,18,4,7,15]trioxatriazacyclotetracosine-6,16,22,23,27,30(7H,16aH)-hexone


Mass: 761.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H51N3O11 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES, 30% PEG3K (pH 9.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.721→31.492 Å / Num. obs: 13998 / % possible obs: 98.93 % / Redundancy: 5.1 % / Biso Wilson estimate: 20.18 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.056 / Rrim(I) all: 0.137 / Net I/σ(I): 9.4
Reflection shellResolution: 1.721→1.78 Å / Rmerge(I) obs: 1.047 / Num. unique obs: 1239 / CC1/2: 0.189 / Rpim(I) all: 0.962 / Rrim(I) all: 0.962

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.721→31.49 Å / SU ML: 0.217 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.4648
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 652 4.66 %
Rwork0.2146 13346 -
obs0.2164 13998 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.49 Å2
Refinement stepCycle: LAST / Resolution: 1.721→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 55 97 998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051930
X-RAY DIFFRACTIONf_angle_d0.83971259
X-RAY DIFFRACTIONf_chiral_restr0.0519129
X-RAY DIFFRACTIONf_plane_restr0.0081162
X-RAY DIFFRACTIONf_dihedral_angle_d24.9692351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.721-1.780.4717500.37871239X-RAY DIFFRACTION93
1.78-1.850.355730.3091301X-RAY DIFFRACTION99
1.85-1.940.3582760.26361300X-RAY DIFFRACTION99
1.94-2.040.2631750.22351308X-RAY DIFFRACTION100
2.04-2.170.3053590.23381327X-RAY DIFFRACTION100

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