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- PDB-9kg9: Crystal structure of the PIN1 and fragment 18 complex. -

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Basic information

Entry
Database: PDB / ID: 9kg9
TitleCrystal structure of the PIN1 and fragment 18 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 / beta-catenin binding / synapse organization / 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
: / 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: 1.55 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 8, 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)19,6019
Polymers18,1851
Non-polymers1,4168
Water2,738152
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)68.247, 68.247, 79.324
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-A1EFP / 3-methoxythiophene-2-carboxylic acid


Mass: 158.175 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O3S / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.93 Å3/Da / Density % sol: 58.06 %
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 PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.55→59.1 Å / Num. obs: 30932 / % possible obs: 98.9 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 0.87 / Net I/σ(I): 16.2 / Num. measured all: 382346
Reflection shellResolution: 1.55→1.64 Å / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.743 / Num. measured all: 56200 / Num. unique obs: 4492 / CC1/2: 0.922 / Rpim(I) all: 0.217 / Rrim(I) all: 0.775 / Χ2: 0.63 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→47.39 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 2011 6.51 %
Rwork0.197 --
obs0.1983 30868 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 90 152 1406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191287
X-RAY DIFFRACTIONf_angle_d1.691719
X-RAY DIFFRACTIONf_dihedral_angle_d9.537216
X-RAY DIFFRACTIONf_chiral_restr0.063164
X-RAY DIFFRACTIONf_plane_restr0.017232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.29271410.28332026X-RAY DIFFRACTION100
1.59-1.640.25881420.25852078X-RAY DIFFRACTION100
1.64-1.680.24161400.24382050X-RAY DIFFRACTION100
1.68-1.740.30641440.22842081X-RAY DIFFRACTION100
1.74-1.80.25091420.21082063X-RAY DIFFRACTION100
1.8-1.870.2591430.19852060X-RAY DIFFRACTION100
1.87-1.960.30461400.24252047X-RAY DIFFRACTION99
1.96-2.060.26291470.20652079X-RAY DIFFRACTION100
2.06-2.190.2341450.18452092X-RAY DIFFRACTION100
2.19-2.360.23361430.19192066X-RAY DIFFRACTION100
2.36-2.60.21231460.19712088X-RAY DIFFRACTION100
2.6-2.970.19591530.19252123X-RAY DIFFRACTION100
2.97-3.740.19021260.1861783X-RAY DIFFRACTION84
3.75-47.390.18321590.18052221X-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)
13.32950.6168-1.86854.1262-2.12913.6182-0.40740.5766-0.4679-0.87080.3976-0.34080.10880.57990.03440.2942-0.10680.01910.2516-0.06620.3369-14.524516.84252.1203
21.03760.12-0.19180.30910.23650.5688-0.19230.240.2674-0.2080.2398-0.2096-0.33860.10950.00510.2849-0.10340.02030.244-0.01250.2765-16.720423.94841.424
32.20730.9262-0.62520.9857-0.35152.00630.15930.1084-0.4870.2169-0.0505-0.38960.15310.5589-0.02470.2329-0.0316-0.04590.2513-0.02420.288-15.010217.52189.5144
41.8439-0.83430.16311.89160.06111.55080.0056-0.1923-0.225-0.05110.07770.27860.3592-0.1941-0.04160.1966-0.06240.00790.20190.02140.163-31.039516.841718.0824
52.45510.2674-0.43873.29312.25892.97860.0830.0261-0.4221-0.0530.03420.44740.441-0.7367-0.01470.1802-0.0499-0.04260.4017-0.02820.2569-45.190823.14579.5115
60.3110.1678-0.60490.1292-0.40651.1937-0.0578-0.03060.22980.0050.11490.1199-0.0383-0.9312-0.02330.14120.01940.00540.38790.01330.2395-45.405129.930313.3555
73.59340.07421.63110.3524-0.05971.6253-0.09710.32130.1698-0.17480.0444-0.0228-0.13390.18180.10070.1792-0.03670.00820.19860.00550.1978-30.065131.34169.4859
82.98860.6748-0.63740.1850.01490.62040.0916-0.50780.1440.0834-0.1356-0.24980.05360.2054-0.05520.1349-0.0378-0.00430.20190.00730.16-29.48130.508821.0903
90.5044-0.576-0.48230.93630.53121.4571-0.08110.093-0.21720.0465-0.08960.20510.4192-0.39330.15150.2386-0.09270.0130.2407-0.01170.2021-33.03214.00615.9078
101.6587-0.2330.39270.9399-0.09591.6131-0.09180.0774-0.014-0.06640.0363-0.01980.1412-0.06250.06270.1751-0.03850.00810.1704-0.00090.1668-27.780818.62812.9154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 62 )
5X-RAY DIFFRACTION5chain 'A' and (resid 63 through 72 )
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 81 )
7X-RAY DIFFRACTION7chain 'A' and (resid 82 through 98 )
8X-RAY DIFFRACTION8chain 'A' and (resid 99 through 110 )
9X-RAY DIFFRACTION9chain 'A' and (resid 111 through 140 )
10X-RAY DIFFRACTION10chain 'A' and (resid 141 through 163 )

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