[English] 日本語
Yorodumi
- PDB-3d1v: Crystal structure of human PNP complexed with 2-mercapto(3H) quin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d1v
TitleCrystal structure of human PNP complexed with 2-mercapto(3H) quinazolinone
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE / DRUG DESIGN / SYNCHROTRON / EMPIRICAL SCORING FUNCTION / 2-MERCAPTO-4(3H) QUINAZOLINONE / Acetylation / Disease mutation / Glycosyltransferase / Polymorphism
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 / Ribavirin ADME / IMP catabolic process / guanosine phosphorylase activity / nucleoside binding / allantoin metabolic process / Purine catabolism / Purine salvage / 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 / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-mercapto(3H)quinazolinone / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDe Azevedo Jr., W.F. / Basso, L.A. / Santos, D.S.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2008
Title: Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function
Authors: Timmers, L.F. / Caceres, R.A. / Vivan, A.L. / Gava, L.M. / Dias, R. / Ducati, R.G. / Basso, L.A. / Santos, D.S. / de Azevedo, W.F.
History
DepositionMay 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6515
Polymers32,1851
Non-polymers4664
Water1,24369
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)97,95415
Polymers96,5553
Non-polymers1,39912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area8800 Å2
ΔGint-180 kcal/mol
Surface area30930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.666, 138.666, 159.379
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

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


Mass: 32184.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NP, PNP / Production host: Escherichia coli (E. coli)
References: UniProt: P00491, purine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-D1V / 2-mercapto(3H)quinazolinone / 2-sulfanylquinazolin-4(3H)-one


Mass: 178.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6N2OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 4.92 Å3/Da / Density % sol: 75 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.3
Details: 0.05M CITRATE BUFFER, 19%AMMONIUM SULPHATE, PH 5.30, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 16, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.431 Å / Relative weight: 1
ReflectionResolution: 2.7→56.531 Å / Num. obs: 16763 / % possible obs: 90.1 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rsym value: 0.099 / Net I/σ(I): 6.6
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.375 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M73

1m73


Resolution: 2.7→42.18 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.454 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.382 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The distance of the C-N bond between PRO146 and LEU147 on chain A is 1.91 Angstrom. The distance of the C-N bond between ALA196 and GLY197 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The distance of the C-N bond between PRO146 and LEU147 on chain A is 1.91 Angstrom. The distance of the C-N bond between ALA196 and GLY197 on chain A is 1.63 Angstrom. The distance of the C-N bond between PRO198 and SER199 on chain A is 1.68 Angstrom. The distance of the C-N bond between SER220 and THR221 on chain A is 1.20 Angstrom. The distance of the C-N bond between PRO223 and GLU224 on chain A is 1.18 Angstrom.
RfactorNum. reflection% reflectionSelection details
Rfree0.27745 816 5 %RANDOM
Rwork0.22113 ---
obs0.22394 15376 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.179 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 27 69 2347
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 55 -
Rwork0.386 1138 -
obs--99.67 %

+
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