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- PDB-5cr7: Human cytosolic 5'-nucleotidase II in complex with N-(9H-Purin-6-... -

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Basic information

Entry
Database: PDB / ID: 5cr7
TitleHuman cytosolic 5'-nucleotidase II in complex with N-(9H-Purin-6-yl)-3-(3-pyrrol-1-ylphenyl)benzamide
ComponentsCytosolic purine 5'-nucleotidase
KeywordsHYDROLASE / complex
Function / homology
Function and homology information


nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity ...nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Ribavirin ADME / IMP catabolic process / IMP metabolic process / Purine catabolism / allantoin metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase / Purine 5'-nucleotidase / 5' nucleotidase family / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Chem-5WO / ACETATE ION / PHOSPHATE ION / Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAghajari, N. / Preeti, P.
Citation
Journal: J.Med.Chem. / Year: 2015
Title: Identification of Noncompetitive Inhibitors of Cytosolic 5'-Nucleotidase II Using a Fragment-Based Approach.
Authors: Marton, Z. / Guillon, R. / Krimm, I. / Rahimova, R. / Egron, D. / Jordheim, L.P. / Aghajari, N. / Dumontet, C. / Perigaud, C. / Lionne, C. / Peyrottes, S. / Chaloin, L.
#1: Journal: Biochem. Pharmacol. / Year: 2013
Title: Identification and characterization of inhibitors of cytoplasmic 5'-nucleotidase cN-II issued from virtual screening.
Authors: Jordheim, L.P. / Marton, Z. / Rhimi, M. / Cros-Perrial, E. / Lionne, C. / Peyrottes, S. / Dumontet, C. / Aghajari, N. / Chaloin, L.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosolic purine 5'-nucleotidase
B: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,80332
Polymers127,9152
Non-polymers2,88830
Water3,567198
1
A: Cytosolic purine 5'-nucleotidase
B: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
B: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,60664
Polymers255,8314
Non-polymers5,77560
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area29930 Å2
ΔGint-234 kcal/mol
Surface area74980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.650, 123.880, 90.580
Angle α, β, γ (deg.)90.00, 115.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytosolic purine 5'-nucleotidase / Cytosolic 5'-nucleotidase II


Mass: 63957.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C2, NT5B, NT5CP, PNT5 / Plasmid: P28A-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA2 / References: UniProt: P49902, 5'-nucleotidase

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Non-polymers , 6 types, 228 molecules

#2: Chemical ChemComp-5WO / ~{N}-(7~{H}-purin-6-yl)-3-(3-pyrrol-1-ylphenyl)benzamide


Mass: 380.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H16N6O
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: ammonium acetate, Bis-Tris, 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→50.9 Å / Num. obs: 31229 / % possible obs: 98 % / Redundancy: 2.9 % / Net I/σ(I): 7.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J2C

2j2c


Resolution: 2.9→45.372 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 1808 4.99 %0.05
Rwork0.22 ---
obs0.2223 36201 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→45.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7420 0 172 198 7790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117832
X-RAY DIFFRACTIONf_angle_d1.34410559
X-RAY DIFFRACTIONf_dihedral_angle_d15.4172853
X-RAY DIFFRACTIONf_chiral_restr0.0511108
X-RAY DIFFRACTIONf_plane_restr0.0061338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7601-2.83470.37211390.29212639X-RAY DIFFRACTION98
2.8347-2.91810.33311400.28132653X-RAY DIFFRACTION99
2.9181-3.01220.30751410.25582683X-RAY DIFFRACTION99
3.0122-3.11990.33421380.25782626X-RAY DIFFRACTION99
3.1199-3.24480.30291410.2392668X-RAY DIFFRACTION99
3.2448-3.39240.29721390.22962658X-RAY DIFFRACTION99
3.3924-3.57120.23321390.21142641X-RAY DIFFRACTION98
3.5712-3.79480.23981390.19792645X-RAY DIFFRACTION98
3.7948-4.08760.2271380.19392625X-RAY DIFFRACTION98
4.0876-4.49870.2351390.17822654X-RAY DIFFRACTION98
4.4987-5.14880.21891390.18372632X-RAY DIFFRACTION98
5.1488-6.4840.26021380.23372630X-RAY DIFFRACTION97
6.484-45.37770.25811380.2282639X-RAY DIFFRACTION96

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