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- PDB-1qpf: FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-709,858 -

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Basic information

Entry
Database: PDB / ID: 1qpf
TitleFK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-709,858
ComponentsPROTEIN (FK506-BINDING PROTEIN)
KeywordsISOMERASE / IMMUNOPHILIN-DRUG COMPLEX / CIS-TRANS ISOMERASE / PEPTIDYL-PROLYL 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 / regulation of amyloid precursor protein catabolic process / heart trabecula formation ...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 / regulation of amyloid precursor protein catabolic process / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / 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
C32-O-(1-ETHYL-INDOL-5-YL)ASCOMYCIN / heptyl beta-D-glucopyranoside / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBecker, J.W. / Rotonda, J.
Citation
Journal: J.Med.Chem. / Year: 1999
Title: 32-Indolyl ether derivatives of ascomycin: three-dimensional structures of complexes with FK506-binding protein.
Authors: Becker, J.W. / Rotonda, J. / Cryan, J.G. / Martin, M. / Parsons, W.H. / Sinclair, P.J. / Wiederrecht, G. / Wong, F.
#1: Journal: Transplantation / Year: 1998
Title: A Tacrolimus-Related Immunosuppressant with Biochemical Properties Distinct from Those of Tacrolimus.
Authors: Peterson, L.B. / Cryan, J.G. / Rosa, R. / Martin, M.M. / Wilusz, M.B. / Sinclair, P.J. / Wong, F. / Parsons, J.N. / O'Keefe, S.J. / Parsons, W.H. / Wyvratt, M. / Sigal, N.H. / Williamson, A. ...Authors: Peterson, L.B. / Cryan, J.G. / Rosa, R. / Martin, M.M. / Wilusz, M.B. / Sinclair, P.J. / Wong, F. / Parsons, J.N. / O'Keefe, S.J. / Parsons, W.H. / Wyvratt, M. / Sigal, N.H. / Williamson, A.R. / Wiederrecht, G.J.
#2: Journal: Transplantation / Year: 1998
Title: A Tacrolimus-Related Immunosuppressant with Reduced Toxicity.
Authors: Dumont, F.J. / Koprak, S. / Staruch, M.J. / Talento, A. / Koo, G. / Dasilva, C. / Sinclair, P.J. / Wong, F. / Woods, J. / Barker, J. / Pivnichny, J. / Singer, I. / H Sigal, N. / Williamson, ...Authors: Dumont, F.J. / Koprak, S. / Staruch, M.J. / Talento, A. / Koo, G. / Dasilva, C. / Sinclair, P.J. / Wong, F. / Woods, J. / Barker, J. / Pivnichny, J. / Singer, I. / H Sigal, N. / Williamson, A.R. / Parsons, W.H. / Wyvratt, M.
#3: Journal: Bioorg.Med.Chem.Lett. / Year: 1996
Title: Preparation and in Vitro Activities of Naphthyl and Indolyl Ether Derivatives of the Fk-506 Related Immunosuppressive Macrolide Ascomycin.
Authors: Sinclair, P.J. / Wong, F. / Staruch, M.J. / Wiederrecht, G. / Parsons, W.H. / Dumont, F. / Wyvratt, M.
History
DepositionMay 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (FK506-BINDING PROTEIN)
D: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8225
Polymers23,6732
Non-polymers2,1493
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules

A: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules

D: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules

D: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,64310
Polymers47,3464
Non-polymers4,2976
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
crystal symmetry operation5_564y,-x+y+1,z-1/61
crystal symmetry operation8_566x-y,-y+1,-z+11
Buried area10900 Å2
ΔGint-42 kcal/mol
Surface area18840 Å2
MethodPISA
3
A: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules

A: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1006
Polymers23,6732
Non-polymers2,4274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
MethodPQS
4
D: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules

D: PROTEIN (FK506-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5434
Polymers23,6732
Non-polymers1,8702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
MethodPQS
Unit cell
Length a, b, c (Å)74.260, 74.260, 236.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein PROTEIN (FK506-BINDING PROTEIN)


Mass: 11836.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62942
#2: Chemical ChemComp-858 / C32-O-(1-ETHYL-INDOL-5-YL)ASCOMYCIN / L-709,858


Mass: 935.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H78N2O12
#3: Sugar ChemComp-B7G / heptyl beta-D-glucopyranoside / HEPTYL-BETA-D-GLUCOPYRANOSIDE / heptyl beta-D-glucoside / heptyl D-glucoside / heptyl glucoside


Type: D-saccharide / Mass: 278.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26O6
IdentifierTypeProgram
heptyl-b-D-GlucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growpH: 5.6
Details: AMMOMIUM SULFATE, BETA-HEPTYL- D-GLUCOPYRANOSIDE, POTASSIUM PHOSPHATE, pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
147 %satammonium sulfate1reservoir
20.2 %beta-heptyl D-glucopyranoside1reservoir
30.10 Mpotassium phosphate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
21
31
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
Detector
TypeIDDetectorDate
SIEMENS1AREA DETECTORMar 4, 1992
SIEMENS2AREA DETECTORMar 11, 1992
SIEMENS3AREA DETECTORMar 30, 1992
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.26→20 Å / Num. obs: 13529 / % possible obs: 71.2 % / Observed criterion σ(I): 0 / Redundancy: 3.86 % / Biso Wilson estimate: 27.21 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 26.63
Reflection shellResolution: 2.26→2.4 Å / Redundancy: 1.54 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 2.41 / % possible all: 33

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROTEIN PORTION OF PDB ENTRY 1FKD

1fkd


Resolution: 2.5→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: A POSTERIORI / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1105 10.2 %RANDOM
Rwork0.243 ---
obs0.243 10793 76.3 %-
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-20 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 153 57 1874
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
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
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.347 61 9.4 %
Rwork0.34 589 -
obs--47.1 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / σ(F): 2 / % reflection Rfree: 10.2 % / Rfactor obs: 0.2436 / Rfactor Rfree: 0.3096
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.347 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.34

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