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- PDB-9ke9: Crystal structure of the PIN1 and fragment 22 complex. -

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Basic information

Entry
Database: PDB / ID: 9ke9
TitleCrystal structure of the PIN1 and fragment 22 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 / cytoplasm / cytosol
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
: / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
DepositionNov 4, 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

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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)19,0526
Polymers18,1851
Non-polymers8675
Water1,02757
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)70.266, 70.266, 79.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 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
#2: Chemical ChemComp-A1BDV / (2H-1,3-benzodioxol-5-yl)methanol / piperonyl alcohol


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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: 3.12 Å3/Da / Density % sol: 60.59 %
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: SSRF / Beamline: BL18U1 / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 22916 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.049 / Rrim(I) all: 0.159 / Χ2: 1.227 / Net I/σ(I): 4 / Num. measured all: 248825
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.75-1.7810.71.84611370.9280.9810.5931.940.516100
1.78-1.8110.81.43711250.8790.9670.4591.510.582100
1.81-1.8510.51.31811210.8970.9720.4261.3870.597100
1.85-1.8911.11.42711470.9410.9850.4461.4960.643100
1.89-1.9310.21.42711260.8780.9670.4891.5111.816100
1.93-1.9710.73.20911050.8940.9721.0363.3751.42100
1.97-2.0211.40.67511370.9550.9890.2080.7070.797100
2.02-2.0711.40.58611390.9710.9930.1820.6140.913100
2.07-2.1411.20.52811140.9680.9920.1650.5540.952100
2.14-2.210.80.38711510.9790.9950.1230.4061.019100
2.2-2.2810.30.52511320.9470.9860.1770.5551.8299.9
2.28-2.38110.30211260.9840.9960.0960.3171.065100
2.38-2.4811.30.23311530.9910.9980.0720.2441.109100
2.48-2.6111.40.19411240.9880.9970.060.2041.195100
2.61-2.78110.17411810.9870.9970.0550.1831.287100
2.78-2.9911.10.13311340.9930.9980.0420.1391.446100
2.99-3.29110.1111700.9940.9990.0350.1161.598100
3.29-3.77110.10511550.9950.9990.0330.1112.395100
3.77-4.7510.10.08111810.9960.9990.0260.0852.101100
4.75-50100.07412580.9960.9990.0250.0781.36599.8

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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: 2.25→33.32 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 1108 9.89 %
Rwork0.2106 --
obs0.2135 11204 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→33.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 21 57 1278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081245
X-RAY DIFFRACTIONf_angle_d1.0171664
X-RAY DIFFRACTIONf_dihedral_angle_d9.799206
X-RAY DIFFRACTIONf_chiral_restr0.052163
X-RAY DIFFRACTIONf_plane_restr0.011213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.350.34521350.31591239X-RAY DIFFRACTION99
2.35-2.470.2851340.25041214X-RAY DIFFRACTION99
2.47-2.630.32821370.26081236X-RAY DIFFRACTION100
2.63-2.830.32741380.24811249X-RAY DIFFRACTION100
2.83-3.110.27421390.22811260X-RAY DIFFRACTION100
3.11-3.560.25811390.20961270X-RAY DIFFRACTION100
3.56-4.490.19661380.17321281X-RAY DIFFRACTION100
4.49-33.320.1891480.19521347X-RAY DIFFRACTION100
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)
12.68761.3875-0.03941.491-0.91791.71630.01180.15710.2662-0.2451-0.01390.3181-0.0544-0.6036-0.03430.5645-0.1869-0.00730.53370.03760.500616.2914-21.1313.8004
22.9528-0.7232-0.73971.2593-0.65923.0096-0.12010.033-0.1128-0.25390.1127-0.3053-0.02280.83960.01640.2909-0.10760.02480.6264-0.05950.384537.8344-27.20311.8118
33.1614-1.68180.67271.3272-0.03853.3608-0.1865-0.0860.0578-0.12150.18970.0105-0.45450.4915-0.02490.388-0.18830.00350.4862-0.01720.344331.2577-19.843615.9297
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 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 163 )

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