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- PDB-7zsl: human purine nucleoside phosphorylase in complex with JS-196 -

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Basic information

Entry
Database: PDB / ID: 7zsl
Titlehuman purine nucleoside phosphorylase in complex with JS-196
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 / Purine salvage / Purine catabolism / allantoin metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / positive regulation of alpha-beta T cell differentiation / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / 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 / cytoplasm / cytosol
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-JTO / DI(HYDROXYETHYL)ETHER / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,51428
Polymers192,9296
Non-polymers3,58522
Water17,042946
1
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,24514
Polymers96,4653
Non-polymers1,78011
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-82 kcal/mol
Surface area29870 Å2
MethodPISA
2
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,26914
Polymers96,4653
Non-polymers1,80411
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-107 kcal/mol
Surface area29740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.120, 185.100, 79.180
Angle α, β, γ (deg.)90.000, 119.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEUAA3 - 2843 - 284
21ASNASNLEULEUBB3 - 2843 - 284
12GLYGLYPROPROAA4 - 2854 - 285
22GLYGLYPROPROCC4 - 2854 - 285
13GLYGLYLEULEUAA4 - 2844 - 284
23GLYGLYLEULEUDD4 - 2844 - 284
14GLYGLYPROPROAA4 - 2854 - 285
24GLYGLYPROPROEE4 - 2854 - 285
15GLYGLYLEULEUAA4 - 2844 - 284
25GLYGLYLEULEUFF4 - 2844 - 284
16GLYGLYLEULEUBB4 - 2844 - 284
26GLYGLYLEULEUCC4 - 2844 - 284
17GLYGLYLEULEUBB4 - 2844 - 284
27GLYGLYLEULEUDD4 - 2844 - 284
18GLYGLYPROPROBB4 - 2834 - 283
28GLYGLYPROPROEE4 - 2834 - 283
19GLYGLYLEULEUBB4 - 2844 - 284
29GLYGLYLEULEUFF4 - 2844 - 284
110GLYGLYLEULEUCC4 - 2844 - 284
210GLYGLYLEULEUDD4 - 2844 - 284
111GLYGLYPROPROCC4 - 2854 - 285
211GLYGLYPROPROEE4 - 2854 - 285
112GLYGLYLEULEUCC4 - 2844 - 284
212GLYGLYLEULEUFF4 - 2844 - 284
113GLYGLYLEULEUDD4 - 2844 - 284
213GLYGLYLEULEUEE4 - 2844 - 284
114GLYGLYLEULEUDD4 - 2844 - 284
214GLYGLYLEULEUFF4 - 2844 - 284
115GLYGLYLEULEUEE4 - 2844 - 284
215GLYGLYLEULEUFF4 - 2844 - 284

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 32154.854 Da / Num. of mol.: 6
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

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Non-polymers , 5 types, 968 molecules

#2: Chemical
ChemComp-JTO / [2-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)sulfanyl]phenoxy]methylphosphonic acid


Mass: 353.290 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H12N3O5PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 946 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.3 M magnesium chloride, 0.3 M calcium chloride, 20% w/v PEG 8000, 40% v/v ethylene glycol, 0.1 M MES/Imidazol, pH 6.0
PH range: 6

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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: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 156419 / % possible obs: 85.8 % / Redundancy: 3.56 % / CC1/2: 0.97 / Net I/σ(I): 13.26
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 6131 / CC1/2: 0.442

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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: 1.8→38.76 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 1565 1 %RANDOM
Rwork0.2251 ---
obs0.2255 154865 86.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 91.5 Å2 / Biso mean: 27.5 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12684 0 225 955 13864
Biso mean--32.84 34.21 -
Num. residues----1637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01313266
X-RAY DIFFRACTIONr_bond_other_d0.0350.01712400
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.6618022
X-RAY DIFFRACTIONr_angle_other_deg2.3121.58128435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71151654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33521.462684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.262152119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1941595
X-RAY DIFFRACTIONr_chiral_restr0.0790.21651
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215055
X-RAY DIFFRACTIONr_gen_planes_other0.0120.023189
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A85430.07
12B85430.07
21A84800.07
22C84800.07
31A85230.07
32D85230.07
41A86520.06
42E86520.06
51A83860.08
52F83860.08
61B84840.07
62C84840.07
71B85590.06
72D85590.06
81B85230.06
82E85230.06
91B84070.07
92F84070.07
101C83420.07
102D83420.07
111C84910.07
112E84910.07
121C82940.07
122F82940.07
131D84040.08
132E84040.08
141D82880.07
142F82880.07
151E83540.07
152F83540.07
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 62 -
Rwork0.348 6071 -
all-6133 -
obs--45.59 %

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