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- PDB-7qgm: Human CD73 (ecto 5'-nucleotidase) in complex with MRS4598 (a 3-me... -

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Basic information

Entry
Database: PDB / ID: 7qgm
TitleHuman CD73 (ecto 5'-nucleotidase) in complex with MRS4598 (a 3-methyl-CMPCP derivative, compound 16 in paper) in the closed state (crystal form III)
Components5'-nucleotidase
KeywordsHYDROLASE / en / e5nt / ecto-nucleotidase / inhibitor
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; 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
Chem-BOI / 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsStrater, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Activity Relationship of 3-Methylcytidine-5'-alpha , beta-methylenediphosphates as CD73 Inhibitors.
Authors: Scortichini, M. / Idris, R.M. / Moschutz, S. / Keim, A. / Salmaso, V. / Dobelmann, C. / Oliva, P. / Losenkova, K. / Irjala, H. / Vaittinen, S. / Sandholm, J. / Yegutkin, G.G. / Strater, N. / ...Authors: Scortichini, M. / Idris, R.M. / Moschutz, S. / Keim, A. / Salmaso, V. / Dobelmann, C. / Oliva, P. / Losenkova, K. / Irjala, H. / Vaittinen, S. / Sandholm, J. / Yegutkin, G.G. / Strater, N. / Junker, A. / Muller, C.E. / Jacobson, K.A.
History
DepositionDec 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: 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 1.2Oct 11, 2023Group: Data collection / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / struct
Item: _audit_author.name / _struct.title
Revision 1.3Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0055
Polymers62,2781
Non-polymers7274
Water00
1
A: 5'-nucleotidase
hetero molecules

A: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,00910
Polymers124,5562
Non-polymers1,4538
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area2930 Å2
ΔGint-125 kcal/mol
Surface area39870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.989, 98.185, 234.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 62277.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Production host: Homo sapiens (human) / References: UniProt: P21589, 5'-nucleotidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-BOI / [[(2~{R},3~{S},4~{R},5~{R})-5-[(4~{E})-4-[(4-chlorophenyl)methoxyimino]-3-methyl-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid


Mass: 555.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24ClN3O11P2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 10 mM MRS4598, 10 microM ZnCl2, 10 % PEG 3.350, 0.1 M BisTris pH 5.6, 10 mM MRS4598, 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: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.9→48.05 Å / Num. obs: 14569 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 89.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.059 / Rrim(I) all: 0.206 / Net I/σ(I): 8.9 / Num. measured all: 175782 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-3.0812.93.4532967123070.6490.993.5940.799.9
8.7-48.0510.40.05363956170.9980.0160.05531.999.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4h2i

4h2i


Resolution: 2.9→47.98 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2941 735 5.08 %
Rwork0.2608 13743 -
obs0.2627 14478 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.24 Å2 / Biso mean: 109.3644 Å2 / Biso min: 60.92 Å2
Refinement stepCycle: final / Resolution: 2.9→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 62 0 4080
Biso mean--107.19 --
Num. residues----516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.120.47071140.41562710282499
3.12-3.440.39381130.349627452858100
3.44-3.940.33361620.288127142876100
3.94-4.960.29241520.23472739289199
4.96-47.980.24861940.223628353029100
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)
14.5877-0.22181.92263.2435-0.87117.67330.50420.718-0.7241-0.2306-0.15610.0323-0.09660.46130.00780.41890.1165-0.0220.3315-0.1790.6623-22.65222.0068-16.1135
22.26420.4769-0.18052.75210.7715.5438-0.24840.064-0.2339-0.21040.1816-0.1414-0.441.047-0.1070.5409-0.0560.12391.3912-0.0980.6709-19.043419.6761-48.3943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 334 )A27 - 334
2X-RAY DIFFRACTION2chain 'A' and (resid 335 through 548 )A335 - 548

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