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- PDB-3d1v: Crystal structure of human PNP complexed with 2-mercapto(3H) quin... -

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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 / nucleoside binding / guanosine phosphorylase activity / Purine catabolism / allantoin metabolic process / Purine salvage / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / purine ribonucleoside salvage / nucleobase-containing compound metabolic process / positive regulation of alpha-beta T cell differentiation / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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

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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

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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 %

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