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- PDB-1fkf: ATOMIC STRUCTURE OF FKBP-FK506, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT... -

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Basic information

Entry
Database: PDB / ID: 1fkf
TitleATOMIC STRUCTURE OF FKBP-FK506, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX
ComponentsFK506 BINDING PROTEIN
KeywordsISOMERASE
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
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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsVanduyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
Citation
Journal: Science / Year: 1991
Title: Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex.
Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
#1: Journal: Nature / Year: 1990
Title: Molecular Cloning and Overexpression of the Human Fk506-Binding Protein Fkbp
Authors: Standaert, R.F. / Galat, A. / Verdine, G.L. / Schreiber, S.L.
History
DepositionMay 7, 1991Processing site: BNL
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: FK506 BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6412
Polymers11,8371
Non-polymers8041
Water1,42379
1
A: FK506 BINDING PROTEIN
hetero molecules

A: FK506 BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2814
Polymers23,6732
Non-polymers1,6082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)58.070, 58.070, 55.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-125-

HOH

21A-153-

HOH

31A-175-

HOH

41A-182-

HOH

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Components

#1: Protein FK506 BINDING PROTEIN


Mass: 11836.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P62942
#2: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal grow
*PLUS
pH: 5.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein-FK506 complex1drop
21.7 M1reservoir(NH4)2SO4
30.1 Mphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 10855 / % possible obs: 99 % / Num. measured all: 69770 / Rmerge(I) obs: 0.0539

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.7→10 Å / Rfactor Rwork: 0.17
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 57 79 968
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2.8
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / σ(I): 2 / Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg

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