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- PDB-1ula: APPLICATION OF CRYSTALLOGRAPHIC AND MODELING METHODS IN THE DESIG... -

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Entry
Database: PDB / ID: 1ula
TitleAPPLICATION OF CRYSTALLOGRAPHIC AND MODELING METHODS IN THE DESIGN OF PURINE NUCLEOSIDE PHOSPHORYLASE INHIBITORS
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsPENTOSYLTRANSFERASE
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 / inosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / nucleotide biosynthetic 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 / inosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / nucleotide biosynthetic process / urate biosynthetic process / Ribavirin ADME / IMP catabolic process / nucleoside binding / guanosine phosphorylase activity / Purine catabolism / allantoin metabolic process / Purine salvage / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / 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
Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.75 Å
AuthorsEalick, S.E. / Rule, S.A. / Carter, D.C. / Greenhough, T.J. / Babu, Y.S. / Cook, W.J. / Habash, J. / Helliwell, J.R. / Stoeckler, J.D. / Parksjunior, R.E. ...Ealick, S.E. / Rule, S.A. / Carter, D.C. / Greenhough, T.J. / Babu, Y.S. / Cook, W.J. / Habash, J. / Helliwell, J.R. / Stoeckler, J.D. / Parksjunior, R.E. / Chen, S.-F. / Bugg, C.E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors.
Authors: Ealick, S.E. / Babu, Y.S. / Bugg, C.E. / Erion, M.D. / Guida, W.C. / Montgomery, J.A. / Secrist 3rd., J.A.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Three-Dimensional Structure of Human Erythrocytic Purine Nucleoside Phosphorylase at 3.2 Angstroms Resolution
Authors: Ealick, S.E. / Rule, S.A. / Carter, D.C. / Greenhough, T.J. / Babu, Y.S. / Cook, W.J. / Habash, J. / Helliwell, J.R. / Stoeckler, J.D. / Parksjunior, R.E. / Chen, S.-F. / Bugg, C.E.
#2: Journal: J.Biol.Chem. / Year: 1981
Title: Crystallization and Preliminary X-Ray Investigation of Human Erythrocyte Purine Nucleoside Phosphorylase
Authors: Cook, W.J. / Ealick, S.E. / Bugg, C.E. / Stoeckler, J.D. / Parksjunior, R.E.
History
DepositionNov 5, 1991Processing site: BNL
SupersessionJan 15, 1993ID: 2PNP
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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Assembly

Deposited unit
A: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3773
Polymers32,1851
Non-polymers1922
Water0
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)97,1319
Polymers96,5553
Non-polymers5766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8350 Å2
ΔGint-137 kcal/mol
Surface area34560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)142.900, 142.900, 165.200
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 /


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.04 Å3/Da / Density % sol: 75.61 %
Crystal grow
*PLUS
Method: unknown

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.202 / Highest resolution: 2.75 Å
Refinement stepCycle: LAST / Highest resolution: 2.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 10 0 2268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_deg3.5

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