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- PDB-2q5a: human Pin1 bound to L-PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 2q5a
Titlehuman Pin1 bound to L-PEPTIDE
Components
  • Five residue peptide
  • Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE/ISOMERASE INHIBITOR / ISOMERASE WW domain / 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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / mitogen-activated protein kinase kinase binding / 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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / mitogen-activated protein kinase kinase binding / 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 / postsynaptic cytosol / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / negative regulation of protein binding / positive regulation of GTPase activity / peptidyl-prolyl cis-trans isomerase activity / regulation of cytokinesis / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / phosphoprotein binding / Negative regulators of DDX58/IFIH1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / negative regulation of ERK1 and ERK2 cascade / regulation of protein stability / negative regulation of protein catabolic process / beta-catenin binding / tau protein binding / ISG15 antiviral mechanism / 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
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
3,6,9,12,15,18-HEXAOXAICOSANE / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNoel, J.P. / Zhang, Y.
CitationJournal: Acs Chem.Biol. / Year: 2007
Title: Structural basis for high-affinity peptide inhibition of human Pin1.
Authors: Zhang, Y. / Daum, S. / Wildemann, D. / Zhou, X.Z. / Verdecia, M.A. / Bowman, M.E. / Lucke, C. / Hunter, T. / Lu, K.P. / Fischer, G. / Noel, J.P.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionJun 26, 2007ID: 2ITI
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,6263
Polymers19,3312
Non-polymers2941
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.842, 68.842, 79.513
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 / Rotamase Pin1 / PPIase Pin1


Mass: 18524.525 Da / Num. of mol.: 1 / Mutation: R14A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: HELA / Gene: PIN1 / Plasmid: pet28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Protein/peptide Five residue peptide


Mass: 806.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Chemical ChemComp-16P / 3,6,9,12,15,18-HEXAOXAICOSANE


Mass: 294.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: M Ammonium Sulfate, 1% PEG400, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2005 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→33 Å / Num. all: 35684 / Num. obs: 34360 / % possible obs: 96.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Net I/σ(I): 44.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.17 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→33 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.445 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25235 1705 5 %RANDOM
Rwork0.23238 ---
obs0.23334 32653 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 20 167 1391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211250
X-RAY DIFFRACTIONr_angle_refined_deg1.3832.0011674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38122.58658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30515211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8171513
X-RAY DIFFRACTIONr_chiral_restr0.0860.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02948
X-RAY DIFFRACTIONr_nbd_refined0.20.2540
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.227
X-RAY DIFFRACTIONr_mcbond_it0.9451.5751
X-RAY DIFFRACTIONr_mcangle_it1.49221168
X-RAY DIFFRACTIONr_scbond_it2.2233574
X-RAY DIFFRACTIONr_scangle_it3.4794.5506
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 128 -
Rwork0.3 2202 -
obs--93.65 %

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