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- PDB-8vjd: Human R14A Pin1 covalently bound to inhibitor 158F10 in P21 21 21... -

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Basic information

Entry
Database: PDB / ID: 8vjd
TitleHuman R14A Pin1 covalently bound to inhibitor 158F10 in P21 21 21 space group
Components
  • Inhibitor 158F10
  • Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE/INHIBITOR / Destabilizing Inhbitor / PPIase / Structure-Activity Relationship / Drug Design / ISOMERASE / ISOMERASE-INHIBITOR complex
Function / homology
Function and homology information


cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / postsynaptic cytosol / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / negative regulation of protein binding / positive regulation of GTPase activity / peptidyl-prolyl cis-trans isomerase activity / regulation of cytokinesis / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / phosphoprotein binding / Negative regulators of DDX58/IFIH1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / negative regulation of ERK1 and ERK2 cascade / regulation of protein stability / negative regulation of protein catabolic process / beta-catenin binding / tau protein binding / ISG15 antiviral mechanism / neuron differentiation / positive regulation of canonical Wnt signaling pathway / positive regulation of protein phosphorylation / regulation of gene expression / midbody / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / ciliary basal body / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. ...: / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsRodriguez, I. / Blaha, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS107479 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA168517 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA285114 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Targeted degradation of Pin1 by protein-destabilizing compounds.
Authors: Alboreggia, G. / Udompholkul, P. / Rodriguez, I. / Blaha, G. / Pellecchia, M.
History
DepositionJan 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
C: Inhibitor 158F10
D: Inhibitor 158F10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,48615
Polymers37,9684
Non-polymers1,51711
Water4,774265
1
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
C: Inhibitor 158F10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8879
Polymers18,9842
Non-polymers9037
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-69 kcal/mol
Surface area8250 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
D: Inhibitor 158F10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5996
Polymers18,9842
Non-polymers6154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-43 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.000, 62.030, 93.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Peptidyl-prolyl cis-trans isomerase Pin1 / PPIase Pin1 / Rotamase Pin1


Mass: 18467.473 Da / Num. of mol.: 2 / Mutation: R14A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q13526, peptidylprolyl isomerase
#2: Protein/peptide Inhibitor 158F10


Mass: 516.612 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: HEPES-NaOH, Ammonium sulfate, PEG400, DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.57→46.71 Å / Num. obs: 49405 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Net I/σ(I): 17.6
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2375 / Rpim(I) all: 0.304

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
BOSdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→46.71 Å / SU ML: 0.1658 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2177 1990 4.03 %
Rwork0.1987 47353 -
obs0.1995 49343 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.25 Å2
Refinement stepCycle: LAST / Resolution: 1.57→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 167 265 2742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592549
X-RAY DIFFRACTIONf_angle_d0.86153415
X-RAY DIFFRACTIONf_chiral_restr0.052333
X-RAY DIFFRACTIONf_plane_restr0.0074434
X-RAY DIFFRACTIONf_dihedral_angle_d18.0723963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.27061450.25073289X-RAY DIFFRACTION99.42
1.61-1.650.24321340.21793337X-RAY DIFFRACTION100
1.65-1.70.23091400.21533333X-RAY DIFFRACTION99.94
1.7-1.760.25111430.21673347X-RAY DIFFRACTION99.97
1.76-1.820.27521360.21773366X-RAY DIFFRACTION100
1.82-1.890.23231400.20743353X-RAY DIFFRACTION99.97
1.89-1.980.20781470.20523336X-RAY DIFFRACTION99.89
1.98-2.080.21861400.20033380X-RAY DIFFRACTION100
2.08-2.210.22671380.2033375X-RAY DIFFRACTION100
2.21-2.380.22831420.20783385X-RAY DIFFRACTION99.97
2.38-2.620.2411430.20443370X-RAY DIFFRACTION99.86
2.62-30.21691400.21413429X-RAY DIFFRACTION99.83
3-3.780.19251520.18323446X-RAY DIFFRACTION99.97
3.78-46.710.20181500.17943607X-RAY DIFFRACTION99.92

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