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- PDB-6tvg: Human CD73 (ecto 5'-nucleotidase) in complex with AMPCP in the op... -

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Basic information

Entry
Database: PDB / ID: 6tvg
TitleHuman CD73 (ecto 5'-nucleotidase) in complex with AMPCP in the open state
Components5'-nucleotidase, ecto (CD73), isoform CRA_a
KeywordsHYDROLASE / eN / e5NT / ecto-nucleotidase / nucleotide
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 / GMP 5'-nucleotidase activity ...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 / GMP 5'-nucleotidase activity / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / AMP catabolic process / Nicotinate metabolism / Purine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / leukocyte cell-cell adhesion / DNA metabolic process / response to ATP / : / calcium ion homeostasis / side of membrane / Purinergic signaling in leishmaniasis infection / ATP metabolic process / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / metal ion binding / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 5'-nucleotidase / 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.48 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 26, 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 ...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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-nucleotidase, ecto (CD73), isoform CRA_a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0836
Polymers60,4641
Non-polymers6195
Water9,890549
1
A: 5'-nucleotidase, ecto (CD73), isoform CRA_a
hetero molecules

A: 5'-nucleotidase, ecto (CD73), isoform CRA_a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,16712
Polymers120,9292
Non-polymers1,23810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4400 Å2
ΔGint-211 kcal/mol
Surface area39310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.259, 131.268, 66.213
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
Components on special symmetry positions
IDModelComponents
11A-1020-

HOH

21A-1185-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 5'-nucleotidase, ecto (CD73), isoform CRA_a / Ecto-5'-nucleotidase


Mass: 60464.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, hCG_401111 / Production host: Escherichia coli (E. coli)
References: UniProt: Q53Z63, UniProt: P21589*PLUS, 5'-nucleotidase

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Non-polymers , 5 types, 554 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AP2 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER


Mass: 425.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N5O9P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 49.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris pH 7.8, 10 % PEG6000, 30 mM AMPCP, 10 % DMSO, 10 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.89429 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89429 Å / Relative weight: 1
ReflectionResolution: 1.477→47.19 Å / Num. obs: 98145 / % possible obs: 99.4 % / Redundancy: 4.96 % / Biso Wilson estimate: 10.7 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.116 / Net I/σ(I): 12
Reflection shellResolution: 1.477→1.53 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4759 / CC1/2: 0.554 / Rrim(I) all: 0.993

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS2016data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4h2g

4h2g


Resolution: 1.48→47.19 Å / SU ML: 0.1415 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.8985
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1674 4896 4.99 %
Rwork0.1278 93178 -
obs0.1298 98074 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.9 Å2
Refinement stepCycle: LAST / Resolution: 1.48→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 0 31 549 4639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744326
X-RAY DIFFRACTIONf_angle_d0.98595918
X-RAY DIFFRACTIONf_chiral_restr0.0813671
X-RAY DIFFRACTIONf_plane_restr0.0064783
X-RAY DIFFRACTIONf_dihedral_angle_d17.80811633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.490.28641660.23973009X-RAY DIFFRACTION97.63
1.49-1.510.24391610.21473060X-RAY DIFFRACTION99.97
1.51-1.530.2521780.193115X-RAY DIFFRACTION99.82
1.53-1.550.2431590.18033091X-RAY DIFFRACTION99.75
1.55-1.570.20261690.16393094X-RAY DIFFRACTION99.76
1.57-1.590.20311750.15983025X-RAY DIFFRACTION99.78
1.59-1.610.22631690.15893115X-RAY DIFFRACTION99.88
1.61-1.640.2091620.15173097X-RAY DIFFRACTION99.91
1.64-1.660.21811700.1463107X-RAY DIFFRACTION99.82
1.66-1.690.19671520.1443103X-RAY DIFFRACTION99.79
1.69-1.720.19641460.13783096X-RAY DIFFRACTION99.69
1.72-1.750.20951730.13193106X-RAY DIFFRACTION99.94
1.75-1.780.15321700.12763092X-RAY DIFFRACTION99.94
1.78-1.820.16471600.11333131X-RAY DIFFRACTION99.88
1.82-1.860.1691680.11343100X-RAY DIFFRACTION99.97
1.86-1.90.16711420.11093128X-RAY DIFFRACTION99.79
1.9-1.950.15511500.10893122X-RAY DIFFRACTION99.94
1.95-20.15411420.10763140X-RAY DIFFRACTION99.85
2-2.060.13621800.10473090X-RAY DIFFRACTION99.79
2.06-2.130.1451600.10513135X-RAY DIFFRACTION99.91
2.13-2.210.1451590.10293144X-RAY DIFFRACTION99.85
2.21-2.290.15921520.10363132X-RAY DIFFRACTION99.7
2.29-2.40.1531760.10493112X-RAY DIFFRACTION99.67
2.4-2.530.1351910.10553103X-RAY DIFFRACTION99.43
2.53-2.680.15081460.11273160X-RAY DIFFRACTION99.04
2.68-2.890.16881560.1163120X-RAY DIFFRACTION98.64
2.89-3.180.15981610.12663118X-RAY DIFFRACTION98.06
3.18-3.640.14751670.13063100X-RAY DIFFRACTION97.35
3.64-4.590.14171620.12213107X-RAY DIFFRACTION95.81
4.59-47.190.18191740.16323126X-RAY DIFFRACTION92.39

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