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- PDB-1fkh: DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP L... -

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Entry
Database: PDB / ID: 1fkh
TitleDESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS, AND THE X-RAY CRYSTAL STRUCTURES OF THEIR COMPLEXES WITH FKBP12
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 / transforming growth factor beta receptor binding / cytoplasmic side of membrane / 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 / transforming growth factor beta receptor binding / cytoplasmic side of membrane / 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 / regulation of amyloid precursor protein catabolic process / signaling receptor inhibitor activity / 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 / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / protein maturation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 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 / cytoplasm / cytosol
Similarity search - Function
Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-SBX / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsHolt, D.A. / Luengo, J.I. / Yamashita, D.S. / Oh, H.-J. / Konialian, A.L. / Yen, H.-K. / Rozamus, L.W. / Brandt, M. / Bossard, M.J. / Levy, M.A. ...Holt, D.A. / Luengo, J.I. / Yamashita, D.S. / Oh, H.-J. / Konialian, A.L. / Yen, H.-K. / Rozamus, L.W. / Brandt, M. / Bossard, M.J. / Levy, M.A. / Eggleston, D.S. / Stout, T.J. / Liang, J. / Schultz, L.W. / Clardy, J.
Citation
Journal: J.Am.Chem.Soc. / Year: 1993
Title: DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS AND THE X-RAY CRYSTAL-STRUCTURES OF THEIR COMPLEXES WITH FKBP12.
Authors: Holt, D.A. / Luengo, J.I. / Yamashita, D.S. / Oh, H.J. / Konialian, A.L. / Yen, H.K. / Rozamus, L.W. / Brandt, M. / Bossard, M.J. / Levy, M.A. / Eggleston, D.S. / Liang, J. / Schultz, L.W. / ...Authors: Holt, D.A. / Luengo, J.I. / Yamashita, D.S. / Oh, H.J. / Konialian, A.L. / Yen, H.K. / Rozamus, L.W. / Brandt, M. / Bossard, M.J. / Levy, M.A. / Eggleston, D.S. / Liang, J. / Schultz, L.W. / Stout, T.J. / Clardy, J.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Atomic Structures of the Human Immunophilin Fkbp-12 Complexes with Fk506 and Rapamycin
Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
History
DepositionAug 5, 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: 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

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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)12,2922
Polymers11,8371
Non-polymers4561
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.450, 43.380, 77.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-SBX / 1-CYCLOHEXYL-3-PHENYL-1-PROPYL-1-(3,3-DIMETHYL-1,2-DIOXYPENTYL)-2-PIPERIDINE CARBOXYLATE


Mass: 455.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H41NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
31.6-1.8 Msodium/potassium phosphate1reservoir
1protein-drug complex1drop0.003ml
2HEPES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 25 Å / Num. obs: 6335 / % possible obs: 98 % / Num. measured all: 18441 / Rmerge(I) obs: 0.082

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.95→10 Å / Rfactor Rwork: 0.161 / Rfactor obs: 0.161
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 33 351 1406
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.161 / Num. reflection obs: 6251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 7.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3
X-RAY DIFFRACTIONx_dihedral_angle_d1.2
X-RAY DIFFRACTIONx_dihedral_angle_deg

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