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- PDB-2nd5: Lysine dimethylated FKBP12 -

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Basic information

Entry
Database: PDB / ID: 2nd5
TitleLysine dimethylated FKBP12
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / lysine / salt bridge / methylation
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / 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 / I-SMAD binding ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / 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 / I-SMAD binding / signaling receptor inhibitor activity / regulation of amyloid precursor protein catabolic process / 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 / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / calcium channel regulator activity / protein maturation / T cell activation / peptidyl-prolyl cis-trans isomerase activity / sarcoplasmic reticulum / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / 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 / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHattori, Y. / Sebera, J. / Sychrovsky, V. / Furuita, K. / Sugiki, T. / Ohki, I. / Ikegami, T. / Kobayashi, N. / Tanaka, Y. / Fujiwara, T. / Kojima, C.
CitationJournal: To be Published
Title: NMR Observation of Protein Surface Salt Bridges at Neutral pH
Authors: Hattori, Y. / Sebera, J. / Sychrovsky, V. / Furuita, K. / Sugiki, T. / Ohki, I. / Ikegami, T. / Kobayashi, N. / Tanaka, Y. / Fujiwara, T. / Kojima, C.
History
DepositionMay 5, 2016Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP1A


Theoretical massNumber of molelcules
Total (without water)12,4251
Polymers12,4251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A / FKBP-12 / Immunophilin FKBP12


Mass: 12425.317 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1412D 1H-1H NOESY
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HN(CA)CO
1813D HNCO
1913D HBHA(CO)NH
11013D C(CO)NH
11113D H(CCO)NH
11213D (H)CCH-TOCSY
11313D 1H-15N TOCSY
11413D 1H-15N NOESY
11513D 1H-13C NOESY aliphatic
11613D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1.2 mM [U-99% 13C; U-99% 15N] entity-1, 30 mM sodium chloride-2, 3 mM DTT-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity-1[U-99% 13C; U-99% 15N]1
30 mMsodium chloride-21
3 mMDTT-31
Sample conditionspH: 6.8 / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MagRO-NMRViewKobayashi, Naohiropeak picking
MagRO-NMRViewKobayashi, Naohirochemical shift assignment
MagRO-NMRViewKobayashi, Naohirodata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3557 / NOE long range total count: 1461 / NOE medium range total count: 555
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 2.4 Å / Maximum upper distance constraint violation: 6 Å / Representative conformer: 1

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