[English] 日本語
Yorodumi
- PDB-9inr: Crystal structure of PIN1 in complex with inhibitor C3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9inr
TitleCrystal structure of PIN1 in complex with inhibitor C3
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / Inhibitor / Complex
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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / regulation of mitotic nuclear division / mitogen-activated protein kinase kinase binding ...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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / regulation of mitotic nuclear division / mitogen-activated protein kinase kinase binding / 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 / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / postsynaptic cytosol / negative regulation of protein binding / positive regulation of GTPase activity / regulation of cytokinesis / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / negative regulation of ERK1 and ERK2 cascade / negative regulation of protein catabolic process / beta-catenin binding / regulation of protein stability / ISG15 antiviral mechanism / tau protein binding / neuron differentiation / positive regulation of canonical Wnt signaling pathway / positive regulation of protein phosphorylation / 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
: / Chem-PE3 / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhang, L.J. / Zhang, L.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Re-Evaluating PIN1 as a Therapeutic Target in Oncology Using Neutral Inhibitors and PROTACs.
Authors: Liu, C. / Chen, Z. / Chen, T. / Song, H. / Shen, J. / Yuan, X. / Xia, S. / Liu, Q. / Chen, Q. / Tian, Q. / Meng, X. / Han, Z. / Dong, X. / Yang, Y. / Cai, L. / Cheng, X. / Jia, Y. / Liu, G. ...Authors: Liu, C. / Chen, Z. / Chen, T. / Song, H. / Shen, J. / Yuan, X. / Xia, S. / Liu, Q. / Chen, Q. / Tian, Q. / Meng, X. / Han, Z. / Dong, X. / Yang, Y. / Cai, L. / Cheng, X. / Jia, Y. / Liu, G. / Li, J. / Ge, J. / Dou, D.
History
DepositionJul 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: audit_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3878
Polymers36,3702
Non-polymers2,0166
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.590, 176.640, 42.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Homo sapiens (human) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Chemical ChemComp-A1D9K / ~{N}-[(2~{S})-3-[1-[4-(4-cyanophenyl)phenyl]-1,2,3-triazol-4-yl]-1-[(3-oxidanylcyclobutyl)amino]-1-oxidanylidene-propan-2-yl]-1-phenyl-cyclopropane-1-carboxamide


Mass: 546.619 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H30N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1 M MES (pH 6.5), 0.2 M Ammonium sulfate, 24~33% (v/v) PEG5K MME

-
Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.93→34.554 Å / Num. obs: 32019 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.188 / Net I/σ(I): 8.1
Reflection shellResolution: 1.93→1.98 Å / Num. unique obs: 2326 / CC1/2: 0.671

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→34.554 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.488 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2295 1578 4.937 %
Rwork0.1929 30384 -
all0.195 --
obs-31962 99.969 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.597 Å2
Baniso -1Baniso -2Baniso -3
1-1.811 Å20 Å2-0 Å2
2---1.498 Å20 Å2
3----0.314 Å2
Refinement stepCycle: LAST / Resolution: 1.93→34.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 138 145 2571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132482
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182259
X-RAY DIFFRACTIONr_angle_refined_deg1.781.7163334
X-RAY DIFFRACTIONr_angle_other_deg1.3941.6575219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2965286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59120.511137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35915406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.031524
X-RAY DIFFRACTIONr_chiral_restr0.1220.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02610
X-RAY DIFFRACTIONr_nbd_refined0.2040.2434
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22068
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21145
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21218
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.228
X-RAY DIFFRACTIONr_nbd_other0.2240.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.210.218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_mcbond_it3.1364.0011156
X-RAY DIFFRACTIONr_mcbond_other3.1324.0011155
X-RAY DIFFRACTIONr_mcangle_it4.0735.9781438
X-RAY DIFFRACTIONr_mcangle_other4.0725.9791439
X-RAY DIFFRACTIONr_scbond_it4.2664.3591326
X-RAY DIFFRACTIONr_scbond_other4.2474.3561315
X-RAY DIFFRACTIONr_scangle_it6.0686.411886
X-RAY DIFFRACTIONr_scangle_other6.0376.4031869
X-RAY DIFFRACTIONr_lrange_it7.24245.6612714
X-RAY DIFFRACTIONr_lrange_other7.19245.5082693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.3011090.2912215X-RAY DIFFRACTION100
1.98-2.0340.2661110.2392175X-RAY DIFFRACTION100
2.034-2.0930.2681070.222070X-RAY DIFFRACTION100
2.093-2.1580.2631020.2072047X-RAY DIFFRACTION100
2.158-2.2290.252980.2111969X-RAY DIFFRACTION100
2.229-2.3070.261130.2051891X-RAY DIFFRACTION99.9003
2.307-2.3940.2021180.1811856X-RAY DIFFRACTION100
2.394-2.4920.254990.1841772X-RAY DIFFRACTION100
2.492-2.6020.224880.1671706X-RAY DIFFRACTION100
2.602-2.7290.2800.1751652X-RAY DIFFRACTION100
2.729-2.8770.225840.181574X-RAY DIFFRACTION100
2.877-3.0510.242710.1811484X-RAY DIFFRACTION100
3.051-3.2620.232870.1881389X-RAY DIFFRACTION100
3.262-3.5230.196650.181307X-RAY DIFFRACTION100
3.523-3.8590.204540.1851242X-RAY DIFFRACTION100
3.859-4.3150.23640.1731101X-RAY DIFFRACTION100
4.315-4.9820.193490.169986X-RAY DIFFRACTION100
4.982-6.10.357310.233868X-RAY DIFFRACTION100
6.1-8.6210.22280.219678X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more