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- PDB-5ui1: Crystal Structure of Human Protein Phosphatase 5C (PP5C) in compl... -

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Basic information

Entry
Database: PDB / ID: 5ui1
TitleCrystal Structure of Human Protein Phosphatase 5C (PP5C) in complex with a triazole inhibitor
ComponentsSerine/threonine-protein phosphatase 5
KeywordsHYSROLASE/HYDROLASE INHIBITOR / Protein Phosphatase / PP5C / Inhibitor Complex / HYSROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


response to arachidonate / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / protein folding chaperone complex / response to morphine / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity ...response to arachidonate / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / protein folding chaperone complex / response to morphine / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity / protein dephosphorylation / ESR-mediated signaling / response to lead ion / ADP binding / Hsp90 protein binding / tau protein binding / Negative regulation of MAPK pathway / MAPK cascade / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic cell cycle / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / lipid binding / DNA-templated transcription / protein-containing complex / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
PPP domain / PP5, C-terminal metallophosphatase domain / : / PPP5 TPR repeat region / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Tetratricopeptide repeat ...PPP domain / PP5, C-terminal metallophosphatase domain / : / PPP5 TPR repeat region / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Tetratricopeptide repeat / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / 4-Layer Sandwich / Tetratricopeptide-like helical domain superfamily / Alpha Beta
Similarity search - Domain/homology
5-phenyl-1H-1,2,3-triazole-4-carboxylic acid / : / Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsChattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Banerjee, S. / Honkanen, R.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)NIH R03MH085702 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS071553 United States
CitationJournal: To Be Published
Title: Crystal Structure Human PP5C in Complex with an Inhibitor
Authors: Chattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Wierzbicki, A. / Honkanen, R.E.
History
DepositionJan 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 5
B: Serine/threonine-protein phosphatase 5
C: Serine/threonine-protein phosphatase 5
D: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,74416
Polymers151,5484
Non-polymers1,19612
Water6,449358
1
A: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1864
Polymers37,8871
Non-polymers2993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1864
Polymers37,8871
Non-polymers2993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1864
Polymers37,8871
Non-polymers2993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1864
Polymers37,8871
Non-polymers2993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.805, 80.708, 91.384
Angle α, β, γ (deg.)87.99, 87.10, 86.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Serine/threonine-protein phosphatase 5 / PP5 / Protein phosphatase T / PPT


Mass: 37887.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP5C, PPP5 / Plasmid: pMAL2CE / Production host: Escherichia coli (E. coli)
References: UniProt: P53041, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-8D4 / 5-phenyl-1H-1,2,3-triazole-4-carboxylic acid


Mass: 189.171 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H7N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20-26% MPD, 4-8% PEG5000MME, 1 mM Manganese chloride, 10 mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.96→91.22 Å / Num. obs: 81256 / % possible obs: 97.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.161 / Net I/σ(I): 5.6
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 11741 / Rpim(I) all: 0.481 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSVERSION November 11, 2013data reduction
SCALAdata scaling
PHASER2.5.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S95

1s95


Resolution: 1.96→91.22 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.543 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24565 4073 5 %RANDOM
Rwork0.21115 ---
obs0.2129 77174 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.135 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.96→91.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10059 0 64 358 10481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910382
X-RAY DIFFRACTIONr_bond_other_d0.0020.029681
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9614042
X-RAY DIFFRACTIONr_angle_other_deg0.903322355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43751249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85824.725510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.244151789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1081544
X-RAY DIFFRACTIONr_chiral_restr0.0680.21488
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022452
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8842.2695008
X-RAY DIFFRACTIONr_mcbond_other0.8842.2685007
X-RAY DIFFRACTIONr_mcangle_it1.5363.3986253
X-RAY DIFFRACTIONr_mcangle_other1.5363.3986254
X-RAY DIFFRACTIONr_scbond_it0.8722.3525374
X-RAY DIFFRACTIONr_scbond_other0.8712.3525375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5213.4847790
X-RAY DIFFRACTIONr_long_range_B_refined2.92217.88711788
X-RAY DIFFRACTIONr_long_range_B_other2.91517.8811778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 301 -
Rwork0.316 5607 -
obs--96.22 %

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