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- PDB-1j4r: FK506 BINDING PROTEIN COMPLEXED WITH FKB-001 -

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Basic information

Entry
Database: PDB / ID: 1j4r
TitleFK506 BINDING PROTEIN COMPLEXED WITH FKB-001
ComponentsFK506-BINDING PROTEIN
KeywordsISOMERASE / ROTAMASE / INHIBITOR
Function / homology
Function and homology information


macrolide binding / activin receptor binding / cytoplasmic side of membrane / signaling receptor inhibitor activity / 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 / terminal cisterna ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / signaling receptor inhibitor activity / 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 / terminal cisterna / ryanodine receptor complex / I-SMAD binding / regulation of amyloid precursor protein catabolic process / protein maturation by protein folding / ventricular cardiac muscle tissue morphogenesis / 'de novo' protein folding / 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 / heart morphogenesis / supramolecular fiber organization / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / T cell activation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / peptidylprolyl isomerase / sarcoplasmic reticulum / 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 / transmembrane transporter binding / amyloid fibril formation / Potential therapeutics for SARS / membrane / cytoplasm / cytosol
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
Chem-001 / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSheriff, S.
CitationJournal: Org.Lett. / Year: 2001
Title: 2-Aryl-2,2-difluoroacetamide FKBP12 ligands: synthesis and X-ray structural studies.
Authors: Dubowchik, G.M. / Vrudhula, V.M. / Dasgupta, B. / Ditta, J. / Chen, T. / Sheriff, S. / Sipman, K. / Witmer, M. / Tredup, J. / Vyas, D.M. / Verdoorn, T.A. / Bollini, S. / Vinitsky, A.
History
DepositionOct 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 300 BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ALTHOUGH THE THREE MOLECULES ARE RELATED TO ONE ANOTHER IN THE ASYMMETRIC UNIT BY NON-CRYSTALLOGRAPHIC 3-FOLD SYMMETRY, THE BIOLOGICAL UNIT IS A MONOMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FK506-BINDING PROTEIN
B: FK506-BINDING PROTEIN
D: FK506-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6689
Polymers35,5103
Non-polymers2,1586
Water2,666148
1
A: FK506-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5533
Polymers11,8371
Non-polymers7172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FK506-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5573
Polymers11,8371
Non-polymers7212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: FK506-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5573
Polymers11,8371
Non-polymers7212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.000, 56.000, 78.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein FK506-BINDING PROTEIN / FKBP / FKBP-1 / Peptidyl-prolyl cis-trans isomerase / PPiase / Rotamase / Immunophilin FKBP12


Mass: 11836.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Chemical ChemComp-001 / 1-[2,2-DIFLUORO-2-(3,4,5-TRIMETHOXY-PHENYL)-ACETYL]-PIPERIDINE-2-CARBOXYLIC ACID 4-PHENYL-1-(3-PYRIDIN-3-YL-PROPYL)-BUTYL ESTER / FKB-001


Mass: 624.715 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H42F2N2O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 39 %
Crystal growpH: 7.5
Details: 2.5 M AMMONIUM SULFATE, 0.1 M HEPES, PH 7.5, CRYOPROTECTANT 20% (V/V) GLYCEROL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MHEPES1reservoirpH7.5
22.5 Mammonium sulfate1reservoir
39.4 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: BRUKER / Detector: AREA DETECTOR / Date: May 22, 1998 / Details: SUPPER 60MM MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→15 Å / Num. obs: 25481 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.8
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 4.4 / % possible all: 92.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 9999 Å / % possible obs: 98 % / Num. measured all: 77913 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 92 % / Num. unique obs: 3970 / Num. measured obs: 8852 / Rmerge(I) obs: 0.155

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FKBP FROM PDB ENTRY 1BL4

1bl4


Resolution: 1.8→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.249 949 3.9 %RANDOM
Rwork0.205 ---
obs0.205 24376 96.8 %-
Displacement parametersBiso mean: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 151 148 2795
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.981.5
X-RAY DIFFRACTIONx_mcangle_it1.532
X-RAY DIFFRACTIONx_scbond_it1.732
X-RAY DIFFRACTIONx_scangle_it2.592.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 137 3.7 %
Rwork0.235 3611 -
obs--90.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.H2OFKB001.TOP
X-RAY DIFFRACTION3FKB001.PARTOPH.SO4
X-RAY DIFFRACTION4PARAM.SO4TOPH.GOL
X-RAY DIFFRACTION5PARAM.GOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 3.9 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
X-RAY DIFFRACTIONx_mcbond_it0.981.5
X-RAY DIFFRACTIONx_scbond_it1.732
X-RAY DIFFRACTIONx_mcangle_it1.532
X-RAY DIFFRACTIONx_scangle_it2.592.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.289 / % reflection Rfree: 3.7 % / Rfactor Rwork: 0.235

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