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- PDB-9jyo: Crystal structure of the Pin1 and fragment 2 complex. -

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Basic information

Entry
Database: PDB / ID: 9jyo
TitleCrystal structure of the Pin1 and fragment 2 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 / Negative regulators of DDX58/IFIH1 signaling / regulation of cytokinesis / peptidylprolyl isomerase / phosphoprotein binding / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / ISG15 antiviral mechanism / synapse organization / negative regulation of protein catabolic process / beta-catenin binding / regulation of protein stability / negative regulation of ERK1 and ERK2 cascade / tau protein binding / positive regulation of protein phosphorylation / neuron differentiation / positive regulation of canonical Wnt signaling pathway / regulation of gene expression / midbody / Regulation of TP53 Activity through Phosphorylation / cellular response to hypoxia / 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: 1.6 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)18,8385
Polymers18,1851
Non-polymers6534
Water3,027168
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)69.512, 69.512, 79.653
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, 172 molecules

#2: Chemical ChemComp-A1EDY / 2-(4-aminophenyl)ethanoic acid / 4-Aminophenylacetic acid


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2 / 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: 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.: 168 / 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: 59.74 %
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: 30114 / % possible obs: 100 % / Redundancy: 19.7 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.034 / Rrim(I) all: 0.149 / Χ2: 1.619 / Net I/σ(I): 4.7 / Num. measured all: 594558
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.6318.20.94515090.9190.9790.2250.9720.548100
1.63-1.6620.10.914720.930.9820.2060.9240.571100
1.66-1.6920.20.79814790.960.990.1810.8190.599100
1.69-1.72200.68914720.9680.9920.1580.7070.634100
1.72-1.7619.70.56714870.9650.9910.1310.5820.689100
1.76-1.820.30.45914680.9810.9950.1050.4710.75100
1.8-1.8519.70.415030.9820.9960.0920.410.866100
1.85-1.920.70.37615020.9850.9960.0850.3850.995100
1.9-1.9519.90.47414820.9790.9950.1110.4871.792100
1.95-2.0220.30.27914830.9890.9970.0640.2861.355100
2.02-2.0919.50.24514970.990.9980.0570.2521.528100
2.09-2.1720.30.21815080.9910.9980.050.2241.649100
2.17-2.2719.20.22514870.9920.9980.0530.2312.132100
2.27-2.3920.60.18415050.9920.9980.0420.1891.919100
2.39-2.5420.30.16315090.9940.9990.0370.1682.049100
2.54-2.7419.80.15515030.9920.9980.0360.162.263100
2.74-3.0119.90.14115330.9960.9990.0320.1452.543100
3.01-3.4520.20.12615220.9960.9990.0290.1292.978100
3.45-4.3418.30.11115590.9960.9990.0270.1143.393100
4.34-5017.80.10516340.9960.9990.0250.1083.10499.9

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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→28.16 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 1984 6.61 %
Rwork0.2007 --
obs0.2021 30016 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 6 168 1374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071228
X-RAY DIFFRACTIONf_angle_d0.8881640
X-RAY DIFFRACTIONf_dihedral_angle_d9.687192
X-RAY DIFFRACTIONf_chiral_restr0.056163
X-RAY DIFFRACTIONf_plane_restr0.01213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.37181390.30671948X-RAY DIFFRACTION99
1.64-1.680.27021410.26441990X-RAY DIFFRACTION100
1.68-1.730.26161420.24871979X-RAY DIFFRACTION100
1.73-1.790.2691440.22791991X-RAY DIFFRACTION100
1.79-1.850.24821380.22591960X-RAY DIFFRACTION100
1.85-1.920.27271330.23731989X-RAY DIFFRACTION100
1.92-2.010.21241400.22521965X-RAY DIFFRACTION100
2.01-2.120.23771470.20431993X-RAY DIFFRACTION100
2.12-2.250.24851440.20592003X-RAY DIFFRACTION100
2.25-2.420.24211410.20471982X-RAY DIFFRACTION100
2.42-2.670.21011410.21382031X-RAY DIFFRACTION100
2.67-3.050.231460.20622014X-RAY DIFFRACTION100
3.05-3.840.21421380.18432054X-RAY DIFFRACTION100
3.84-28.160.18281500.17432133X-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)
11.79790.8020.00161.7383-0.12982.4899-0.28620.0389-0.2387-0.1990.1666-0.45820.25930.31340.08420.3143-0.15340.02860.2483-0.00310.2963-19.154119.91416.5796
22.2504-0.0753-0.91741.3098-0.05861.3565-0.10260.02910.2797-0.21750.12290.0589-0.1424-0.544-0.05920.1657-0.07-0.01340.3920.04910.212-36.698329.590212.8543
31.8005-0.65280.02111.3938-0.17880.9692-0.2349-0.1002-0.0978-0.21010.21850.02370.6464-0.562-0.01380.311-0.21-0.00130.29730.02470.1864-31.136216.757514.6954
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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