[English] 日本語
Yorodumi
- PDB-1qpf: FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-709,858 -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more