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- PDB-1f40: SOLUTION STRUCTURE OF FKBP12 COMPLEXED WITH GPI-1046, A NEUROTROP... -

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Basic information

Entry
Database: PDB / ID: 1f40
TitleSOLUTION STRUCTURE OF FKBP12 COMPLEXED WITH GPI-1046, A NEUROTROPHIC LIGAND
ComponentsFK506 BINDING PROTEIN (FKBP12)
KeywordsISOMERASE
Function / homology
Function and homology information


macrolide binding / activin receptor binding / cytoplasmic side of membrane / signaling receptor inhibitor activity / 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 / terminal cisterna ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / signaling receptor inhibitor activity / 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 / 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 / transmembrane transporter binding / Potential therapeutics for SARS / amyloid fibril formation / membrane / cytosol / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-GPI / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSich, C. / Improta, S. / Cowley, D.J. / Guenet, C. / Merly, J.P. / Teufel, M. / Saudek, V.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: Solution structure of a neurotrophic ligand bound to FKBP12 and its effects on protein dynamics.
Authors: Sich, C. / Improta, S. / Cowley, D.J. / Guenet, C. / Merly, J.P. / Teufel, M. / Saudek, V.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Neurotrophic Immunophilin Ligands Stimulate Structural and Functional Recovery in Neurodegenerative Animal Models
Authors: Steiner, J.P. / Hamilton, G.S. / Ross, D.T. / Valentine, H.L. / Guo, H. / Connolly, M.A. / Liang, S. / Ramsey, C. / Li, J.H. / Huang, W. / Howorth, P. / Soni, R. / Fuller, M. / Sauer, H. / ...Authors: Steiner, J.P. / Hamilton, G.S. / Ross, D.T. / Valentine, H.L. / Guo, H. / Connolly, M.A. / Liang, S. / Ramsey, C. / Li, J.H. / Huang, W. / Howorth, P. / Soni, R. / Fuller, M. / Sauer, H. / Nowotnik, A.C. / Suzdak, P.D.
#2: Journal: Science / Year: 1991
Title: Atomic Structure of FKBP-FK506, an Immunophilin-immunosuppressant Complex
Authors: van Duyne, G.D. / Staendert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
#3: Journal: J.Am.Chem.Soc. / Year: 1993
Title: Design, Synthesis, and Kinetic Evaluation of high-affinity FKBP Ligands and the X-ray Structure of their Complexes with FKBP12
Authors: Holt, D.A. / Luengo, J.I. / Yamashita, D.S. / Oh, H.-J. / Konalian, A.L. / Yen, H.-K. / Rozamus, L.W. / Brandt, M. / Bossard, M.J. / Levy, M.A. / Eggleston, D.S. / Lian, J. / Schultz, L.W. / ...Authors: Holt, D.A. / Luengo, J.I. / Yamashita, D.S. / Oh, H.-J. / Konalian, A.L. / Yen, H.-K. / Rozamus, L.W. / Brandt, M. / Bossard, M.J. / Levy, M.A. / Eggleston, D.S. / Lian, J. / Schultz, L.W. / Stout, T.J. / Clardy, J.
#4: Journal: Biochemistry / Year: 1994
Title: 15N NMR Relaxation Studies of the FK506 Binding Protein: Dynamic Effects of Ligand Binding and Implications for Calcinerin Inhibition
Authors: Cheng, J.W. / Lepre, C.A. / Moore, J.M.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FK506 BINDING PROTEIN (FKBP12)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1972
Polymers11,8371
Non-polymers3601
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein FK506 BINDING PROTEIN (FKBP12)


Mass: 11836.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROTEIN COORDINATES WERE TAKEN FROM THE CRYSTAL STRUCTURE BY HOLT ET AL. (1993, PDB ACCESSION CODE 1FKG).
Source: (gene. exp.) Homo sapiens (human) / Organ: BRAIN / Plasmid: PARS-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942
#2: Chemical ChemComp-GPI / (2S)-[3-PYRIDYL-1-PROPYL]-1-[3,3-DIMETHYL-1,2-DIOXOPENTYL]-2-PYRROLIDINECARBOXYLATE / GPI-1046


Mass: 360.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N2O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 13C-separated NOESY
1232D 15N,13C-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM FKBP12 U-15N; 100 mM phosphate buffer; 0.01% NaN390% H2O/10% D2O
20.5 mM FKBP12 U-15N; 1mM GPI-1046; 100 mM phosphate buffer; 0.01% NaN390% H2O/10% D2O
32mM FKBP12 U-15N,13C; 2mM GPI-1046; 100 mM phosphate buffer; 0.01% NaN390% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 6.5 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.1collection
XwinNMR1.1processing
AURELIA2.1Neidig, P.data analysis
Felix97.2data analysis
X-PLOR3.851Brunger A.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures were calculated using a total of 50 ligand-ligand and 18 protein-ligand distance restraints. NOEs involving degenerate protons were incorporated as ambiguous restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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