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- PDB-9jyp: Crystal structure of the PIN1 and fragment 3 complex -

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Basic information

Entry
Database: PDB / ID: 9jyp
TitleCrystal structure of the PIN1 and fragment 3 complex
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / cis-trans isomerase
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 / mitogen-activated protein kinase kinase binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / 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 / mitogen-activated protein kinase kinase binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / 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 / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / postsynaptic cytosol / negative regulation of protein binding / Rho protein signal transduction / regulation of cytokinesis / peptidylprolyl isomerase / Negative regulators of DDX58/IFIH1 signaling / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / beta-catenin binding / negative regulation of protein catabolic process / regulation of protein stability / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / tau protein binding / positive regulation of protein phosphorylation / neuron differentiation / positive regulation of canonical Wnt signaling pathway / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsXiao, Q.J. / Wu, T.T. / Shu, H.L. / Qin, W.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Uncovering druggable hotspots on Pin1 via X-ray crystallographic fragment screening.
Authors: Xiao, Q. / Tang, J. / Shu, H. / Wu, T. / Zhang, H. / Wang, W. / Wang, L. / Qin, W.
History
DepositionOct 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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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 NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9236
Polymers18,1851
Non-polymers7385
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.668, 69.668, 79.223
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18185.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13526, peptidylprolyl isomerase

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-A1EDZ / 4-oxidanylidene-4-thiophen-2-yl-butanoic acid / 3-(2-Thenoyl)propionic acid


Mass: 184.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 2.6M AMMONIUM SULPHATE, 0.1M HEPES BUFFER PH7.5, 1% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 29763 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.033 / Rrim(I) all: 0.145 / Χ2: 1.224 / Net I/σ(I): 4.9 / Num. measured all: 567077
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.6315.31.95114560.90.9730.5132.0190.523100
1.63-1.6617.51.84314780.9240.980.4531.8990.538100
1.66-1.6918.51.7214510.9690.9920.411.7690.556100
1.69-1.7218.61.55714700.9580.9890.3711.6010.598100
1.72-1.76191.44614700.9650.9910.341.4860.601100
1.76-1.819.70.9914760.9830.9960.2281.0160.631100
1.8-1.8519.40.85214600.9860.9960.1970.8750.709100
1.85-1.920.10.89114820.9860.9960.2040.9140.943100
1.9-1.9518.80.73914660.9890.9970.1750.761.361100
1.95-2.02200.46314540.9910.9980.1060.4751.039100
2.02-2.09190.39914990.9930.9980.0930.411.282100
2.09-2.1720.10.29514740.9940.9990.0670.3031.199100
2.17-2.2719.10.2414840.9940.9980.0560.2471.428100
2.27-2.3920.60.19714940.9970.9990.0440.2011.282100
2.39-2.5420.20.15714730.9970.9990.0360.1611.407100
2.54-2.7419.70.13815020.9960.9990.0320.1421.608100
2.74-3.0119.90.10715210.9970.9990.0250.111.702100
3.01-3.45200.08915030.99810.020.0912.043100
3.45-4.3417.80.07615310.99910.0180.0782.49599.9
4.34-50180.0716190.9980.9990.0170.0732.20199.9

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→28.19 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 1982 6.69 %
Rwork0.1873 --
obs0.1892 29630 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 11 195 1404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061232
X-RAY DIFFRACTIONf_angle_d0.9731648
X-RAY DIFFRACTIONf_dihedral_angle_d8.42190
X-RAY DIFFRACTIONf_chiral_restr0.056163
X-RAY DIFFRACTIONf_plane_restr0.01215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.3291370.27841873X-RAY DIFFRACTION96
1.64-1.690.25111350.23211952X-RAY DIFFRACTION99
1.69-1.730.26531360.2311959X-RAY DIFFRACTION100
1.73-1.790.21811360.21941962X-RAY DIFFRACTION99
1.79-1.850.23391410.21641936X-RAY DIFFRACTION99
1.85-1.930.25621460.21261961X-RAY DIFFRACTION100
1.93-2.020.27181370.20211940X-RAY DIFFRACTION100
2.02-2.120.21431430.19051981X-RAY DIFFRACTION100
2.12-2.260.221460.19931983X-RAY DIFFRACTION100
2.26-2.430.21781400.19111978X-RAY DIFFRACTION100
2.43-2.670.22451420.19982009X-RAY DIFFRACTION100
2.67-3.060.20651450.19931986X-RAY DIFFRACTION100
3.06-3.850.19661490.16892030X-RAY DIFFRACTION100
3.86-28.190.20461490.16432098X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.25840.31960.07710.45450.23030.397-0.05450.1279-0.180.0282-0.0312-0.32220.02820.22060.00390.3452-0.16770.00930.24960.00990.3137-15.950820.57643.562
20.5543-0.3147-0.16250.40850.0710.3585-0.01650.06780.0024-0.1114-0.0603-0.08780.5954-0.4759-0.01250.2258-0.1329-0.03070.37540.01450.1769-38.904320.571913.3453
30.565-0.2146-0.26150.41760.18010.32920.0513-0.05690.2282-0.097-0.0025-0.0024-0.1372-0.32450.00010.1576-0.0271-0.00520.31180.040.228-34.424331.26113.6162
40.7689-0.3854-0.16870.76610.1980.6333-0.13-0.0646-0.0078-0.0730.1339-0.01230.5208-0.4556-0.00890.2826-0.1243-0.00640.24680.01790.1895-31.14916.769514.658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 110 )
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 163 )

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