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- PDB-4h4b: Human cytosolic 5'-nucleotidase II in complex with Anthraquinone-... -

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Basic information

Entry
Database: PDB / ID: 4h4b
TitleHuman cytosolic 5'-nucleotidase II in complex with Anthraquinone-2,6- disulfonic acid
ComponentsCytosolic purine 5'-nucleotidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIGH KM 5-PRIME NUCLEOTIDASE / cN-II / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / HYDROLASE-HYDROLASE INHIBITOR 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 / adenosine metabolic process / : / IMP-specific 5'-nucleotidase / : ...nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / adenosine metabolic process / : / IMP-specific 5'-nucleotidase / : / IMP metabolic process / IMP catabolic process / Ribavirin ADME / allantoin metabolic process / Purine catabolism / : / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / metal ion binding / identical protein 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-11H / Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRhimi, M. / Aghajari, N.
CitationJournal: 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
DepositionSep 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,0549
Polymers64,0891
Non-polymers9658
Water1,04558
1
A: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,21636
Polymers256,3564
Non-polymers3,86032
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area18670 Å2
ΔGint-370 kcal/mol
Surface area75780 Å2
MethodPISA
2
A: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,10818
Polymers128,1782
Non-polymers1,93016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area7650 Å2
ΔGint-176 kcal/mol
Surface area39570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.11, 126.83, 130.4
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 64088.930 Da / Num. of mol.: 1
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 (E. coli) / Strain (production host): ROSETTA2(DE) / References: UniProt: P49902, 5'-nucleotidase

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Non-polymers , 5 types, 66 molecules

#2: Chemical ChemComp-11H / 9,10-dioxo-9,10-dihydroanthracene-2,6-disulfonic acid


Mass: 368.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8O8S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: magnesium sulphate and Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979696 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979696 Å / Relative weight: 1
ReflectionResolution: 2.9→90.9 Å / Num. all: 16880 / Num. obs: 16022 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J2C

2j2c


Resolution: 2.9→48.92 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.881 / SU B: 32.255 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 1.971 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 858 5.1 %RANDOM
Rwork0.184 ---
obs0.188 16022 98.6 %-
all-16872 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.302 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2---0.6 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 56 58 3930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223966
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9765363
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91723.011186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45815681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4651526
X-RAY DIFFRACTIONr_chiral_restr0.1140.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212990
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.52325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24723748
X-RAY DIFFRACTIONr_scbond_it2.04231641
X-RAY DIFFRACTIONr_scangle_it3.564.51615
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 60 -
Rwork0.256 993 -
obs--84.92 %
Refinement TLS params.Method: refined / Origin x: -0.0048 Å / Origin y: 24.6682 Å / Origin z: 45.9782 Å
111213212223313233
T0.1353 Å20.0063 Å2-0.0012 Å2-0.0303 Å20.0205 Å2--0.0301 Å2
L1.9735 °20.3131 °2-0.1174 °2-0.5113 °20.051 °2--1.0652 °2
S0.004 Å °0.0635 Å °0.1881 Å °-0.0564 Å °0.0039 Å °0.0726 Å °-0.2324 Å °-0.0335 Å °-0.0079 Å °

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