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- PDB-1fkd: FK-506 BINDING PROTEIN: THREE-DIMENSIONAL STRUCTURE OF THE COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1fkd
TitleFK-506 BINDING PROTEIN: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX WITH THE ANTAGONIST L-685,818
ComponentsFK506 BINDING PROTEINFKBP
KeywordsCIS-TRANS ISOMERASE
Function / homology
Function and homology information


macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / 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 / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / 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 / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / 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
18-HYDROXYASCOMYCIN / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.72 Å
AuthorsBecker, J.W. / Rotonda, J. / Mckeever, B.M.
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: J.Exp.Med. / Year: 1992
Title: The Immunosuppressive and Toxic Effects of Fk-506 are Mechanistically Related: Pharmacology of a Novel Antagonist of Fk-506 and Rapamycin
Authors: Dumont, F.J. / Staruch, M.J. / Koprak, S.L. / Siekierka, J.J. / Lin, C.S. / Harrison, R. / Sewell, T. / Kindt, V.M. / Beattie, T.R. / Wyvratt, M. / Sigal, N.H.
History
DepositionDec 2, 1992Processing 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 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
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)12,6452
Polymers11,8371
Non-polymers8081
Water1,15364
1
A: FK506 BINDING PROTEIN
hetero molecules

A: FK506 BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2894
Polymers23,6732
Non-polymers1,6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
MethodPQS
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)50,5788
Polymers47,3464
Non-polymers3,2324
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 area9630 Å2
ΔGint-41 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.140, 58.140, 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-481-

HOH

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Components

#1: Protein FK506 BINDING PROTEIN / FKBP


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-818 / 18-HYDROXYASCOMYCIN / L-685,818


Mass: 808.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H69NO13
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion
Components of the solutions
*PLUS
Conc.: 57 %sat / Chemical formula: (NH4)2SO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
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 /
RfactorNum. reflection
obs0.181 10312
Refinement stepCycle: LAST / Resolution: 1.72→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 57 64 953
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0340.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0091
X-RAY DIFFRACTIONp_mcangle_it1.5721.5
X-RAY DIFFRACTIONp_scbond_it1.3441
X-RAY DIFFRACTIONp_scangle_it2.1081.5
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.1910.15
X-RAY DIFFRACTIONp_singtor_nbd0.2040.5
X-RAY DIFFRACTIONp_multtor_nbd0.150.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1750.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.43
X-RAY DIFFRACTIONp_staggered_tor12.715
X-RAY DIFFRACTIONp_orthonormal_tor19.320
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.72 Å / Lowest resolution: 8 Å / Num. reflection all: 10312 / σ(F): 0 / Rfactor all: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

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