+Open data
-Basic information
Entry | Database: PDB / ID: 1qpf | ||||||
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Title | FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-709,858 | ||||||
Components | PROTEIN (FK506-BINDING PROTEIN) | ||||||
Keywords | ISOMERASE / IMMUNOPHILIN-DRUG COMPLEX / CIS-TRANS ISOMERASE / PEPTIDYL-PROLYL ISOMERASE | ||||||
Function / homology | Function and homology information signaling receptor inhibitor activity / macrolide binding / activin receptor binding / cytoplasmic side of membrane / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / 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 ...signaling receptor inhibitor activity / macrolide binding / activin receptor binding / cytoplasmic side of membrane / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / 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 / ventricular cardiac muscle tissue morphogenesis / protein maturation by protein folding / 'de novo' protein folding / FK506 binding / channel regulator activity / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / regulation of immune response / regulation of ryanodine-sensitive calcium-release channel activity / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / protein folding / positive regulation of protein binding / regulation of protein localization / protein refolding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / amyloid fibril formation / Potential therapeutics for SARS / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Becker, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qpf.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qpf.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 1qpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qpf_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1qpf_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1qpf_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 1qpf_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/1qpf ftp://data.pdbj.org/pub/pdb/validation_reports/qp/1qpf | HTTPS FTP |
-Related structure data
Related structure data | 1qplC 1fkdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: 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 | #3: Sugar | ChemComp-B7G / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.3 % | ||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 | ||||||||||||||||
Detector |
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Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||
Reflection | Resolution: 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 shell | Resolution: 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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PROTEIN PORTION OF PDB ENTRY 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
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Displacement parameters | Biso mean: 17.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
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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
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Rfactor Rfree: 0.347 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.34 |