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- PDB-3tcz: Human Pin1 bound to cis peptidomimetic inhibitor -

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Basic information

Entry
Database: PDB / ID: 3tcz
TitleHuman Pin1 bound to cis peptidomimetic inhibitor
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE/Inhibitor / PPIase domain / WW domain / Peptidyl-prolyl isomerase / ISOMERASE-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 / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / negative regulation of SMAD protein signal transduction ...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 / regulation of mitotic nuclear division / postsynaptic cytosol / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / protein peptidyl-prolyl isomerization / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / : / positive regulation of GTPase activity / ciliary basal body / regulation of cytokinesis / negative regulation of protein binding / 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 / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / negative regulation of protein catabolic process / neuron differentiation / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / positive regulation of protein phosphorylation / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / : / 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 / Chitinase A; domain 3 - #40 / WW domain ...Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / : / 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 / Chitinase A; domain 3 - #40 / WW domain / WW/rsp5/WWP domain signature. / Chitinase A; domain 3 / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Single Sheet / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-R2Z / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsZhang, M. / Zhang, Y.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Structural and Kinetic Analysis of Prolyl-isomerization/Phosphorylation Cross-Talk in the CTD Code.
Authors: Zhang, M. / Wang, X.J. / Chen, X. / Bowman, M.E. / Luo, Y. / Noel, J.P. / Ellington, A.D. / Etzkorn, F.A. / Zhang, Y.
History
DepositionAug 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,4123
Polymers17,6101
Non-polymers8032
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.389, 69.389, 79.607
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 17609.605 Da / Num. of mol.: 1 / Fragment: UNP residues 6-163 / Mutation: R14A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Chemical ChemComp-R2Z / N~2~-({(1R,2Z)-2-[(2R)-2-(formylamino)-3-(phosphonooxy)propylidene]cyclopentyl}carbonyl)-L-argininamide


Mass: 448.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H29N6O7P
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.9-2.2 M ammonium sulfate, 1% PEG400 at pH 7.5 in 50 mM HEPES buffer, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE DIP100 / Detector: IMAGE PLATE / Date: Apr 22, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 68383 / Rmerge(I) obs: 0.054 / Χ2: 0.94 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 12458 / % possible obs: 93.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.525092.810.0230.822
3.594.5295.310.0240.805
3.143.5994.510.040.915
2.853.1494.810.0640.892
2.652.8594.510.1140.971
2.492.6594.610.1510.947
2.372.4994.410.2350.975
2.262.3794.110.330.991
2.182.2691.710.4051.037
2.12.1884.810.4761.091
ReflectionResolution: 2.1→50 Å / Num. all: 12458 / Num. obs: 11618 / % possible obs: 93.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.054 / Net I/σ(I): 26.4
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.476 / % possible all: 84.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→33.19 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.698 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 1187 10.2 %RANDOM
Rwork0.2234 ---
obs0.2277 11618 93.45 %-
all-12432 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.72 Å2 / Biso mean: 33.3096 Å2 / Biso min: 17.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20.67 Å20 Å2
2--1.34 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 54 87 1305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211242
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9841657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8122.58658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41815215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3011513
X-RAY DIFFRACTIONr_chiral_restr0.0920.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02925
X-RAY DIFFRACTIONr_nbd_refined0.2130.2579
X-RAY DIFFRACTIONr_nbtor_refined0.290.2823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.218
X-RAY DIFFRACTIONr_mcbond_it0.7561.5753
X-RAY DIFFRACTIONr_mcangle_it1.28821161
X-RAY DIFFRACTIONr_scbond_it1.8253559
X-RAY DIFFRACTIONr_scangle_it2.8944.5496
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 72 -
Rwork0.296 585 -
all-657 -
obs--82.75 %

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