[English] 日本語
Yorodumi
- PDB-7zsm: human purine nucleoside phosphorylase in complex with JS-375 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zsm
Titlehuman purine nucleoside phosphorylase in complex with JS-375
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / PNP-inhibitor complex
Function / homology
Function and homology information


nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / nucleotide biosynthetic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine catabolic process / urate biosynthetic process ...nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / nucleotide biosynthetic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine catabolic process / urate biosynthetic process / IMP catabolic process / Ribavirin ADME / guanosine phosphorylase activity / nucleoside binding / allantoin metabolic process / Purine salvage / Purine catabolism / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / positive regulation of alpha-beta T cell differentiation / nucleobase-containing compound metabolic process / phosphate ion binding / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / secretory granule lumen / ficolin-1-rich granule lumen / immune response / response to xenobiotic stimulus / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
Chem-JU9 / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsDjukic, S. / Pachl, P. / Rezacova, P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729European Union
CitationJournal: J.Med.Chem. / Year: 2023
Title: Design, Synthesis, Biological Evaluation, and Crystallographic Study of Novel Purine Nucleoside Phosphorylase Inhibitors.
Authors: Skacel, J. / Djukic, S. / Baszczynski, O. / Kalcic, F. / Bilek, T. / Chalupsky, K. / Kozak, J. / Dvorakova, A. / Tloust'ova, E. / Kral'ova, Z. / Smidkova, M. / Voldrich, J. / Rumlova, M. / ...Authors: Skacel, J. / Djukic, S. / Baszczynski, O. / Kalcic, F. / Bilek, T. / Chalupsky, K. / Kozak, J. / Dvorakova, A. / Tloust'ova, E. / Kral'ova, Z. / Smidkova, M. / Voldrich, J. / Rumlova, M. / Pachl, P. / Brynda, J. / Vuckova, T. / Fabry, M. / Snasel, J. / Pichova, I. / Rezacova, P. / Mertlikova-Kaiserova, H. / Janeba, Z.
History
DepositionMay 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8337
Polymers32,1551
Non-polymers6786
Water50428
1
A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,49821
Polymers96,4653
Non-polymers2,03318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8270 Å2
ΔGint-122 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.530, 142.530, 164.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-305-

CL

-
Components

#1: Protein Purine nucleoside phosphorylase / PNP / Inosine phosphorylase / Inosine-guanosine phosphorylase


Mass: 32154.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNP, NP / Production host: Escherichia coli (E. coli)
References: UniProt: P00491, purine-nucleoside phosphorylase
#2: Chemical ChemComp-JU9 / [(~{E})-2-[4-methoxy-2-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)sulfanyl]phenyl]ethenyl]phosphonic acid


Mass: 379.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N3O5PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.99 Å3/Da / Density % sol: 75.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.5 MAmmonium sulphate, 1M Lithium sulphate, 0.1 M sodium citrate pH 5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 18872 / % possible obs: 99.9 % / Redundancy: 19 % / CC1/2: 1 / Net I/σ(I): 22.38
Reflection shellResolution: 2.65→2.81 Å / Num. unique obs: 2997 / CC1/2: 0.417

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PHB

3phb


Resolution: 2.65→49.39 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.885 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 944 5 %RANDOM
Rwork0.2175 ---
obs0.2188 17927 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 207.78 Å2 / Biso mean: 85.268 Å2 / Biso min: 63.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å2-0 Å2
2--0.2 Å2-0 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 2.65→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 38 28 2215
Biso mean--103.87 81.83 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132235
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152039
X-RAY DIFFRACTIONr_angle_refined_deg1.351.6423041
X-RAY DIFFRACTIONr_angle_other_deg1.2981.5714659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.63221.739115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33815334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5681515
X-RAY DIFFRACTIONr_chiral_restr0.0570.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
LS refinement shellResolution: 2.65→2.716 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.788 68 -
Rwork0.695 1289 -
obs--99.41 %

+
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