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- PDB-6tve: Unliganded human CD73 (5'-nucleotidase) in the open state -

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Basic information

Entry
Database: PDB / ID: 6tve
TitleUnliganded human CD73 (5'-nucleotidase) in the open state
Components5'-nucleotidase
KeywordsHYDROLASE / eN / e5NT / dizinc / ecto-nucleotidase
Function / homology
Function and homology information


thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / AMP catabolic process ...thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / AMP catabolic process / GMP 5'-nucleotidase activity / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Nicotinate metabolism / Purine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / DNA metabolic process / leukocyte cell-cell adhesion / response to ATP / : / Purinergic signaling in leishmaniasis infection / calcium ion homeostasis / ATP metabolic process / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases ...5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsScaletti, E. / Strater, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)STR 477/13-2 Germany
CitationJournal: J.Med.Chem. / Year: 2020
Title: 2-Substituted alpha , beta-Methylene-ADP Derivatives: Potent Competitive Ecto-5'-nucleotidase (CD73) Inhibitors with Variable Binding Modes.
Authors: Bhattarai, S. / Pippel, J. / Scaletti, E. / Idris, R. / Freundlieb, M. / Rolshoven, G. / Renn, C. / Lee, S.Y. / Abdelrahman, A. / Zimmermann, H. / El-Tayeb, A. / Muller, C.E. / Strater, N.
History
DepositionJan 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,53715
Polymers60,4641
Non-polymers1,07214
Water12,340685
1
P: 5'-nucleotidase
hetero molecules

P: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,07330
Polymers120,9292
Non-polymers2,14428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6760 Å2
ΔGint-166 kcal/mol
Surface area39150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.316, 131.380, 66.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 1 molecules P

#1: Protein 5'-nucleotidase / 5'-NT / Ecto-5'-nucleotidase


Mass: 60464.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: construct 2.71 / Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Production host: Escherichia coli (E. coli) / References: UniProt: P21589, 5'-nucleotidase

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Non-polymers , 5 types, 699 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 100 mM Tris pH 7.8, PEG6000, 100 mM Gly-Pro, 10 % DMSO. The Gly-Pro dipeptide was added as part of fragment screening experiment but did not bind to the protein.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.05→32.84 Å / Num. obs: 267271 / % possible obs: 98.5 % / Redundancy: 6.56 % / Biso Wilson estimate: 8.91 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.055 / Net I/σ(I): 15.9
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 5.93 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 12510 / CC1/2: 0.636 / Rrim(I) all: 0.858 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS2015data reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2h2g

2h2g


Resolution: 1.05→32.84 Å / SU ML: 0.0756 / Cross valid method: FREE R-VALUE / Phase error: 10.4204
RfactorNum. reflection% reflection
Rfree0.1327 13442 5.03 %
Rwork0.1176 --
obs0.1184 267195 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.07 Å2
Refinement stepCycle: LAST / Resolution: 1.05→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 53 685 4761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064411
X-RAY DIFFRACTIONf_angle_d0.99776021
X-RAY DIFFRACTIONf_chiral_restr0.0841667
X-RAY DIFFRACTIONf_plane_restr0.007797
X-RAY DIFFRACTIONf_dihedral_angle_d17.56191617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.060.2494170.23887875X-RAY DIFFRACTION93.11
1.06-1.080.23254360.21938213X-RAY DIFFRACTION96.65
1.08-1.090.19924600.19028237X-RAY DIFFRACTION96.9
1.09-1.10.17934850.16988270X-RAY DIFFRACTION97
1.1-1.120.16964590.15398242X-RAY DIFFRACTION97.22
1.12-1.130.15544230.14478300X-RAY DIFFRACTION97.24
1.13-1.150.15774670.13968279X-RAY DIFFRACTION97.55
1.15-1.170.14144190.12948398X-RAY DIFFRACTION97.6
1.17-1.180.14334380.12448352X-RAY DIFFRACTION97.72
1.18-1.20.13644540.12168334X-RAY DIFFRACTION97.93
1.2-1.220.12894320.11878404X-RAY DIFFRACTION98.01
1.22-1.250.13294420.11538384X-RAY DIFFRACTION98.11
1.25-1.270.1324530.10948378X-RAY DIFFRACTION98.29
1.27-1.30.12024190.10528452X-RAY DIFFRACTION98.28
1.3-1.320.1314220.10038403X-RAY DIFFRACTION98.2
1.32-1.360.11114390.09878454X-RAY DIFFRACTION98.68
1.36-1.390.11024320.09688494X-RAY DIFFRACTION98.89
1.39-1.430.11084230.09278510X-RAY DIFFRACTION98.91
1.43-1.470.1034240.09118552X-RAY DIFFRACTION99.22
1.47-1.520.10414680.08818470X-RAY DIFFRACTION99.2
1.52-1.570.09964780.08778525X-RAY DIFFRACTION99.32
1.57-1.630.10764900.0898513X-RAY DIFFRACTION99.49
1.63-1.710.10494400.09288583X-RAY DIFFRACTION99.54
1.71-1.80.10824880.09798570X-RAY DIFFRACTION99.75
1.8-1.910.11984670.09958600X-RAY DIFFRACTION99.76
1.91-2.060.11464720.1038646X-RAY DIFFRACTION99.82
2.06-2.260.1224710.1058671X-RAY DIFFRACTION99.88
2.26-2.590.13674310.11538744X-RAY DIFFRACTION99.91
2.59-3.270.13794340.1268815X-RAY DIFFRACTION99.77
3.27-32.840.15844590.14329085X-RAY DIFFRACTION99.53

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