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- PDB-1yat: IMPROVED CALCINEURIN INHIBITION BY YEAST FKBP12-DRUG COMPLEXES. C... -

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Basic information

Entry
Database: PDB / ID: 1yat
TitleIMPROVED CALCINEURIN INHIBITION BY YEAST FKBP12-DRUG COMPLEXES. CRYSTALLOGRAPHIC AND FUNCTIONAL ANALYSIS
ComponentsFK506 BINDING PROTEIN
KeywordsBINDING PROTEIN
Function / homology
Function and homology information


regulation of homoserine biosynthetic process / Calcineurin activates NFAT / negative regulation of homoserine biosynthetic process / : / macrolide binding / mTORC1-mediated signalling / nonfunctional rRNA decay / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity ...regulation of homoserine biosynthetic process / Calcineurin activates NFAT / negative regulation of homoserine biosynthetic process / : / macrolide binding / mTORC1-mediated signalling / nonfunctional rRNA decay / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / mitochondrion / nucleus / cytoplasm
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
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / FK506-binding protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsRotonda, J. / Becker, J.W.
Citation
Journal: J.Biol.Chem. / Year: 1993
Title: Improved calcineurin inhibition by yeast FKBP12-drug complexes. Crystallographic and functional analysis.
Authors: Rotonda, J. / Burbaum, J.J. / Chan, H.K. / Marcy, A.I. / Becker, J.W.
#1: 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.
History
DepositionJan 6, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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 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 SIX-STRANDED SHEETS ARE DEFINED. STRANDS 1, 2, 3, 4, AND 5 ARE IDENTICAL IN BOTH SHEETS WHILE STRAND 6 IS DIFFERENT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FK506 BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8432
Polymers12,0391
Non-polymers8041
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.681, 79.681, 54.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein FK506 BINDING PROTEIN


Mass: 12038.628 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P20081
#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.: 41 / 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: 4.11 Å3/Da / Density % sol: 70.09 %
Crystal grow
*PLUS
pH: 8.75 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.6 M1reservoir(NH4)2SO4
20.1 MTris-HCl1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 6822 / % possible obs: 98 % / Num. measured all: 57469 / Rmerge(I) obs: 0.0977

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Processing

Software
NameClassification
CORELSrefinement
PROLSQrefinement
RefinementResolution: 2.5→8 Å / σ(F): 0 /
RfactorNum. reflection
obs0.177 6822
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms849 0 57 41 947
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection all: 6822 / σ(F): 0 / Rfactor all: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.018
X-RAY DIFFRACTIONo_angle_d0.04

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