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- PDB-9hd5: Crystal structure of CD73 (ecto-5'-nucleotidase) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9hd5
TitleCrystal structure of CD73 (ecto-5'-nucleotidase) in complex with the AOPCP derivative PSB19427 in the closed state
Components5'-nucleotidase
KeywordsHYDROLASE / ecto-5-nucleotidase / AMP hydrolysis / inhibition / PET tracer
Function / homology
Function and homology information


thymidylate 5'-phosphatase / : / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / adenosine biosynthetic process / inhibition of non-skeletal tissue mineralization / Pyrimidine catabolism / AMP catabolic process ...thymidylate 5'-phosphatase / : / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / adenosine biosynthetic process / inhibition of non-skeletal tissue mineralization / Pyrimidine catabolism / AMP catabolic process / : / IMP-specific 5'-nucleotidase / : / Nicotinate metabolism / Purine catabolism / 5'-nucleotidase / 5'-nucleotidase activity / leukocyte cell-cell adhesion / DNA metabolic process / response to ATP / Purinergic signaling in leishmaniasis infection / ATP metabolic process / calcium ion homeostasis / 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 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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.911 Å
AuthorsStrater, N. / Moschuetz, S. / Dobelmann, C. / Schmies, C.C. / Jacobson, K.A. / Muller, C.E. / Junker, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)JU 2966/2-2 Germany
German Research Foundation (DFG)SFB 1328 Germany
CitationJournal: To Be Published
Title: Positron emission tomography (PET) tracer enables imaging of CD73 expression in cancer
Authors: Dobelmann, C. / Schmies, C.C.
History
DepositionNov 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,3988
Polymers119,7262
Non-polymers1,6726
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-26 kcal/mol
Surface area39960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.635, 233.367, 54.058
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 5'-nucleotidase / 5'-NT / 5'-deoxynucleotidase / Ecto-5'-nucleotidase / IMP-specific 5'-nucleotidase / Thymidylate 5'- ...5'-NT / 5'-deoxynucleotidase / Ecto-5'-nucleotidase / IMP-specific 5'-nucleotidase / Thymidylate 5'-phosphatase


Mass: 59863.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P21589, thymidylate 5'-phosphatase, 5'-nucleotidase, 5'-deoxynucleotidase, 7-methylguanosine nucleotidase, IMP-specific 5'-nucleotidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1IT6 / [[(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-[[4-[1-(2-fluoranylethyl)-1,2,3-triazol-4-yl]phenyl]methyl-propyl-amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid


Mass: 704.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H32ClFN8O9P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 6000, 0.1 M BisTrisPropane pH 7.0, 10 mM PSB19427, 10 microM ZnCl2, 10 mM Tris pH 8.0, 20 % PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.91→49.37 Å / Num. obs: 16993 / % possible obs: 90.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 56.9 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.951 / Rpim(I) all: 0.279 / Rrim(I) all: 0.992 / Net I/σ(I): 5.5
Reflection shellResolution: 2.91→3.08 Å / Rmerge(I) obs: 8.048 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 849 / CC1/2: 0.122 / Rpim(I) all: 2.606 / Rrim(I) all: 8.493

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (18-SEP-2020)refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.911→49.37 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.633
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 978 5.76 %RANDOM
Rwork0.1896 ---
obs0.1942 16993 63.9 %-
Displacement parametersBiso mean: 57.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.2176 Å20 Å20 Å2
2--4.3723 Å20 Å2
3----3.1547 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.911→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 96 118 8188
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088278HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0611229HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2905SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1457HARMONIC5
X-RAY DIFFRACTIONt_it8278HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion20.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1061SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7064SEMIHARMONIC4
LS refinement shellResolution: 2.911→2.99 Å
RfactorNum. reflection% reflection
Rfree0.4649 -3.1 %
Rwork0.2412 344 -
obs--16.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.89570.4511.1944.69941.57071.6307-0.16240.19560.00170.32570.119-0.17830.00870.08070.04340.01850.0475-0.1138-0.12470.0274-0.231921.669113.54997.5404
20.5279-0.7985-0.06336.4060.69331.51260.23890.0603-0.0195-0.3679-0.031-0.2238-0.0374-0.0003-0.20790.201-0.0181-0.0362-0.30690.0504-0.308819.036245.15214.8602
31.5655-0.0924-1.27755.97031.37282.5876-0.2038-0.04290.08170.29790.069-0.17670.2219-0.0670.1348-0.0051-0.06980.0685-0.3231-0.0356-0.365320.316998.430819.4021
40.64181.1376-0.48746.4717-0.12410.37350.36450.0846-0.00770.9188-0.0533-0.1125-0.08230.0269-0.31110.3715-0.12010.08-0.29960.033-0.319718.956166.724122.0388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|333 A|601 - A|602 }
2X-RAY DIFFRACTION2{ A|334 - A|549 }
3X-RAY DIFFRACTION3{ B|1 - B|333 B|601 - B|602 }
4X-RAY DIFFRACTION4{ B|334 - B|549 }

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