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- PDB-1qpl: FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-707,587 -

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Basic information

Entry
Database: PDB / ID: 1qpl
TitleFK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-707,587
ComponentsPROTEIN (FK506-BINDING PROTEIN)
KeywordsISOMERASE / IMMUNOPHILIN-DRUG COMPLEX / CIS-TRANS ISOMERASE / PEPTIDYL-PROLYL ISOMERASE
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
C32-O-(1-METHYL-INDOL-5-YL) 18-HYDROXY-ASCOMYCIN / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBecker, J.W. / Rotonda, J.
Citation
Journal: J.Med.Chem. / Year: 1999
Title: 32-Indolyl ether derivatives of ascomycin: three-dimensional structures of complexes with FK506-binding protein.
Authors: Becker, J.W. / Rotonda, J. / Cryan, J.G. / Martin, M. / Parsons, W.H. / Sinclair, P.J. / Wiederrecht, G. / Wong, F.
#1: Journal: Transplantation / Year: 1998
Title: A Tacrolimus-Related Immunosuppressant with Biochemical Properties Distinct from Those of Tacrolimus.
Authors: Peterson, L.B. / Cryan, J.G. / Rosa, R. / Martin, M.M. / Wilusz, M.B. / Sinclair, P.J. / Wong, F. / Parsons, J.N. / O'Keefe, S.J. / Parsons, W.H. / Wyvratt, M. / Sigal, N.H. / Williamson, A. ...Authors: Peterson, L.B. / Cryan, J.G. / Rosa, R. / Martin, M.M. / Wilusz, M.B. / Sinclair, P.J. / Wong, F. / Parsons, J.N. / O'Keefe, S.J. / Parsons, W.H. / Wyvratt, M. / Sigal, N.H. / Williamson, A.R. / Wiederrecht, G.J.
#2: Journal: Transplantation / Year: 1998
Title: A Tacrolimus-Related Immunosuppressant with Reduced Toxicity.
Authors: Dumont, F.J. / Koprak, S. / Staruch, M.J. / Talento, A. / Koo, G. / Dasilva, C. / Sinclair, P.J. / Wong, F. / Woods, J. / Barker, J. / Pivnichny, J. / Singer, I. / Sigal, N.H. / Williamson, ...Authors: Dumont, F.J. / Koprak, S. / Staruch, M.J. / Talento, A. / Koo, G. / Dasilva, C. / Sinclair, P.J. / Wong, F. / Woods, J. / Barker, J. / Pivnichny, J. / Singer, I. / Sigal, N.H. / Williamson, A.R. / Parsons, W.H. / Wyvratt, M.
#3: Journal: Bioorg.Med.Chem.Lett. / Year: 1996
Title: Preparation and in Vitro Activities of Naphthyl and Indolyl Ether Derivatives of the Fk-506 Related Immunosuppressive Macrolide Ascomycin.
Authors: Sinclair, P.J. / Wong, F. / Staruch, M.J. / Wiederrecht, G. / Parsons, W.H. / Dumont, F. / Wyvratt, M.
History
DepositionMay 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FK506-BINDING PROTEIN)
C: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5474
Polymers23,6732
Non-polymers1,8742
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.740, 119.740, 57.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein PROTEIN (FK506-BINDING PROTEIN)


Mass: 11836.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62942
#2: Chemical ChemComp-587 / C32-O-(1-METHYL-INDOL-5-YL) 18-HYDROXY-ASCOMYCIN / L-709,587


Mass: 937.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C52H76N2O13
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 3.98 Å3/Da / Density % sol: 69.1 %
Crystal growpH: 6.1 / Details: AMMONIUM SULFATE, POTASSIUM PHOSPHATE, pH 6.1
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
139 %satammonium sulfate1reservoir
20.10 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 30, 1991
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→42.33 Å / Num. obs: 12979 / % possible obs: 85.1 % / Observed criterion σ(I): 0 / Redundancy: 6.41 % / Biso Wilson estimate: 68.48 Å2 / Rmerge(I) obs: 0.0585 / Net I/σ(I): 29.28
Reflection shellResolution: 2.5→2.61 Å / % possible all: 57.2
Reflection shell
*PLUS
% possible obs: 57.2 %

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Processing

Software
NameClassification
MERLOTphasing
X-PLORrefinement
X-GENdata scaling
FBSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROTEIN PORTION OF PDB ENTRY 1FKD

1fkd


Resolution: 2.9→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: A POSTERIORI / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.342 903 10.6 %RANDOM
Rwork0.223 ---
obs0.223 8527 93.6 %-
Displacement parametersBiso mean: 59.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-20 Å
Luzzati sigma a0.49 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 134 14 1812
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.342 46 6.4 %
Rwork0.337 675 -
obs--79.9 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19

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