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- PDB-1j4h: crystal structure analysis of the FKBP12 complexed with 000107 sm... -

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Basic information

Entry
Database: PDB / ID: 1j4h
Titlecrystal structure analysis of the FKBP12 complexed with 000107 small molecule
ComponentsFKBP12FKBP1A
KeywordsISOMERASE / Rotamase
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
Chem-SUB / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLi, P. / Ding, Y. / Wang, L. / Wu, B. / Shu, C. / Li, S. / Shen, B. / Rao, Z.
CitationJournal: Biophys.J. / Year: 2003
Title: Design and structure-based study of new potential FKBP12 inhibitors.
Authors: Sun, F. / Li, P. / Ding, Y. / Wang, L. / Bartlam, M. / Shu, C. / Shen, B. / Jiang, H. / Li, S. / Rao, Z.
History
DepositionSep 30, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Dec 27, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FKBP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3132
Polymers11,8371
Non-polymers4771
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.02, 30.38, 42.38
Angle α, β, γ (deg.)90, 110.74, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FKBP12 / FKBP1A / FK506-binding protein


Mass: 11836.508 Da / Num. of mol.: 1
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-SUB / 3-PHENYL-2-{[4-(TOLUENE-4-SULFONYL)-THIOMORPHOLINE-3-CARBONYL]-AMINO}-PROPIONIC ACID ETHYL ESTER / (3R)-4-(P-TOLUENESULFONYL)-1,4-THIAZANE-3-CARBOXYLIC ACID-L-PHENYLALANINE ETHYL ESTER


Type: L-peptide linking / Mass: 476.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N2O5S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: PEG10000, HEPES, pH 6.5, EVAPORATION, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMcacodylic acid sodium1droppH6.5
220 mg/mlprotein1drop
315-27 %PEG100001reservoir
40.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 32811 / Num. obs: 32675 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.291 / Num. unique all: 773 / % possible all: 98.1
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 9478 / Num. measured all: 32811
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 98.1 % / Num. unique obs: 773 / Mean I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
CNS1phasing
RefinementResolution: 1.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.25 970 10.3 %
Rwork0.203 --
all-9487 -
obs-9346 98.5 %
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms831 0 32 137 1000
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.98
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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