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- PDB-2fke: FK-506-BINDING PROTEIN: THREE-DIMENSIONAL STRUCTURE OF THE COMPLE... -

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Basic information

Entry
Database: PDB / ID: 2fke
TitleFK-506-BINDING PROTEIN: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX WITH THE ANTAGONIST L-685,818
ComponentsFK506 BINDING PROTEIN
KeywordsCIS-TRANS ISOMERASE
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: 1.72 Å
AuthorsBecker, J.W. / Mckeever, B.M. / Rotonda, J.
Citation
Journal: J.Biol.Chem. / Year: 1993
Title: FK-506-binding protein: three-dimensional structure of the complex with the antagonist L-685,818.
Authors: Becker, J.W. / Rotonda, J. / McKeever, B.M. / Chan, H.K. / Marcy, A.I. / Wiederrecht, G. / Hermes, J.D. / Springer, J.P.
#1: Journal: Acta Crystallogr.,Sect.C / Year: 1987
Title: Structure of a New Macrocyclic Antibiotic
Authors: Taga, T. / Tanaka, H. / Goto, T. / Tada, S.
History
DepositionJan 27, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 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
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3, AND 4 OF A1 AND A2 BELOW ARE IDENTICAL WHILE STRAND 5 IS DIFFERENT.

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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
Water1,27971
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 operation8_665-y+1,-x+1,-z1
Buried area3440 Å2
ΔGint-8 kcal/mol
Surface area10460 Å2
MethodPISA, PQS
2
A: FK506 BINDING PROTEIN
hetero molecules

A: FK506 BINDING PROTEIN
hetero molecules

A: FK506 BINDING PROTEIN
hetero molecules

A: FK506 BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5628
Polymers47,3464
Non-polymers3,2164
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area9800 Å2
ΔGint-41 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.154, 58.154, 55.445
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-481-

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.: 71 / 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: 37.85 %
Crystal grow
*PLUS
pH: 5.1 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
147 %sat1reservoir(NH4)2SO4
20.1 Mpotassium formate1reservoir
30.02 %1reservoirNaN3

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Data collection

Reflection
*PLUS
Highest resolution: 1.72 Å / Num. obs: 11113 / Num. measured all: 64522 / Rmerge(I) obs: 0.0594

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.72→8 Å / σ(F): 0
Details: THE FOLLOWING RESIDUE HAS DIHEDRAL ANGLES WHICH LIE OUTSIDE THE NORMAL RANGE: PHI PSI OMEGA ALA 81 -135.50 -119.02 -175.46
RfactorNum. reflection
obs0.18 10181
Refinement stepCycle: LAST / Resolution: 1.72→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 57 71 960
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1241
X-RAY DIFFRACTIONp_mcangle_it1.7441.5
X-RAY DIFFRACTIONp_scbond_it1.4891
X-RAY DIFFRACTIONp_scangle_it2.3861.5
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.1880.15
X-RAY DIFFRACTIONp_singtor_nbd0.2040.5
X-RAY DIFFRACTIONp_multtor_nbd0.1560.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1910.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.43
X-RAY DIFFRACTIONp_staggered_tor14.515
X-RAY DIFFRACTIONp_orthonormal_tor17.820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.72 Å / Lowest resolution: 8 Å / Num. reflection all: 10181 / σ(F): 0 / Rfactor all: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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