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- PDB-9kxf: Crystal structure of the PIN1 and fragment 39 complex. -

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Basic information

Entry
Database: PDB / ID: 9kxf
TitleCrystal structure of the PIN1 and fragment 39 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 / Negative regulators of DDX58/IFIH1 signaling / peptidylprolyl isomerase / 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: 1.71 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
DepositionDec 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)18,9015
Polymers18,1851
Non-polymers7164
Water2,810156
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)69.050, 69.050, 78.630
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-A1EHG / ~{N}-(2-fluorophenyl)ethanamide


Mass: 153.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8FNO / 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: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.98 Å3/Da / Density % sol: 58.66 %
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: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.71→32.85 Å / Num. obs: 22959 / % possible obs: 95.8 % / Redundancy: 17.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.026 / Rrim(I) all: 0.106 / Χ2: 0.99 / Net I/σ(I): 19.8 / Num. measured all: 400195
Reflection shellResolution: 1.71→1.75 Å / % possible obs: 100 % / Redundancy: 18.7 % / Rmerge(I) obs: 1.788 / Num. measured all: 32578 / Num. unique obs: 1739 / CC1/2: 0.895 / Rpim(I) all: 0.422 / Rrim(I) all: 1.838 / Χ2: 0.69 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→32.85 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 1150 5.03 %
Rwork0.2129 --
obs0.2146 22849 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 46 156 1366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071238
X-RAY DIFFRACTIONf_angle_d1.0381655
X-RAY DIFFRACTIONf_dihedral_angle_d8.344194
X-RAY DIFFRACTIONf_chiral_restr0.057164
X-RAY DIFFRACTIONf_plane_restr0.01214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.790.35251670.31942779X-RAY DIFFRACTION100
1.79-1.880.38951450.30932696X-RAY DIFFRACTION97
1.88-20.40631170.36192022X-RAY DIFFRACTION73
2-2.150.28231370.25562822X-RAY DIFFRACTION99
2.15-2.370.3231440.26832686X-RAY DIFFRACTION95
2.37-2.710.21831490.2142827X-RAY DIFFRACTION100
2.71-3.420.25311390.20732881X-RAY DIFFRACTION100
3.42-32.850.19121520.1622986X-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)
10.33790.37020.41730.52180.58160.8345-0.11430.0322-0.0648-0.03540.19-0.21450.03940.06460.0110.2829-0.09920.01230.21920.0170.2685-18.876219.74456.399
20.8943-0.2493-0.46610.78390.09230.5048-0.02920.07010.3527-0.13660.0129-0.1692-0.1221-0.2257-0.00430.1423-0.04070.00080.32520.03970.1415-36.450929.396612.4927
30.1513-0.1939-0.20280.2460.26980.3635-0.0735-0.03740.0802-0.05310.08230.01140.3189-0.336-0.00080.3008-0.1068-0.00210.2910.01040.2077-30.968216.573514.539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 163 )

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