[English] 日本語
Yorodumi
- PDB-5ui1: Crystal Structure of Human Protein Phosphatase 5C (PP5C) in compl... -

+
Open data


ID or keywords:

Loading...

-
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


positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / response to arachidonate / peptidyl-threonine dephosphorylation / peptidyl-serine dephosphorylation / proximal dendrite / mitogen-activated protein kinase kinase kinase binding / protein folding chaperone complex / response to morphine / cellular response to cadmium ion / protein-serine/threonine phosphatase ...positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / response to arachidonate / peptidyl-threonine dephosphorylation / peptidyl-serine dephosphorylation / proximal dendrite / mitogen-activated protein kinase kinase kinase binding / protein folding chaperone complex / response to morphine / cellular response to cadmium ion / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphatase activity / phosphoprotein phosphatase activity / protein serine/threonine kinase inhibitor activity / G-protein alpha-subunit binding / protein dephosphorylation / negative regulation of MAPK cascade / Hsp70 protein binding / ESR-mediated signaling / Hsp90 protein binding / response to lead ion / ADP binding / tau protein binding / Negative regulation of MAPK pathway / cellular response to hydrogen peroxide / MAPK cascade / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / double-strand break repair / mitotic cell cycle / perikaryon / microtubule binding / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / DNA-templated transcription / lipid binding / negative regulation of apoptotic process / protein-containing complex binding / protein-containing complex / RNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
PP5, C-terminal metallophosphatase domain / PPP 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 ...PP5, C-terminal metallophosphatase domain / PPP 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
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