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- PDB-7jv8: Human CD73 (ecto 5'-nucleotidase) in complex with compound 35 -

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Basic information

Entry
Database: PDB / ID: 7jv8
TitleHuman CD73 (ecto 5'-nucleotidase) in complex with compound 35
Components5'-nucleotidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 5'-NUCLEOTIDASE / HYDROLASE / PHOSPHATASE / PROTEROS / PROTEROS BIOSTRUCTURES GMBH / HYDROLASE-HYDROLASE INHIBITOR complex
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 / ATP metabolic process / Purinergic signaling in leishmaniasis infection / 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; domain 2 / 5'-Nucleotidase, C-terminal domain / 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 signature 1. / 5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 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-VPD / 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsGibbons, P. / Du, X.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Orally Bioavailable Small-Molecule CD73 Inhibitor (OP-5244) Reverses Immunosuppression through Blockade of Adenosine Production.
Authors: Du, X. / Moore, J. / Blank, B.R. / Eksterowicz, J. / Sutimantanapi, D. / Yuen, N. / Metzger, T. / Chan, B. / Huang, T. / Chen, X. / Chen, Y. / Duong, F. / Kong, W. / Chang, J.H. / Sun, J. / ...Authors: Du, X. / Moore, J. / Blank, B.R. / Eksterowicz, J. / Sutimantanapi, D. / Yuen, N. / Metzger, T. / Chan, B. / Huang, T. / Chen, X. / Chen, Y. / Duong, F. / Kong, W. / Chang, J.H. / Sun, J. / Zavorotinskaya, T. / Ye, Q. / Junttila, M.R. / Ndubaku, C. / Friedman, L.S. / Fantin, V.R. / Sun, D.
History
DepositionAug 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: 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 18, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 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
B: 5'-nucleotidase
C: 5'-nucleotidase
D: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,89920
Polymers235,0644
Non-polymers2,83516
Water9,026501
1
A: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4755
Polymers58,7661
Non-polymers7094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4755
Polymers58,7661
Non-polymers7094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4755
Polymers58,7661
Non-polymers7094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4755
Polymers58,7661
Non-polymers7094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.876, 102.354, 129.609
Angle α, β, γ (deg.)90.000, 103.220, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA25 - 5493 - 527
21SERSERBB25 - 5493 - 527
12PHEPHEAA25 - 5483 - 526
22PHEPHECC25 - 5483 - 526
13SERSERAA25 - 5493 - 527
23SERSERDD25 - 5493 - 527
14SERSERBB25 - 5493 - 527
24SERSERCC25 - 5493 - 527
15SERSERBB25 - 5493 - 527
25SERSERDD25 - 5493 - 527
16PHEPHECC25 - 5483 - 526
26PHEPHEDD25 - 5483 - 526

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 58765.887 Da / Num. of mol.: 4 / Mutation: N53D, N333D, N403D
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, 5'-nucleotidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-VPD / 6-chloro-N-cyclopentyl-1-{5-O-[(2R)-1-hydroxy-3-methoxy-2-phosphonopropan-2-yl]-beta-D-ribofuranosyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine / OP-0105244


Mass: 537.888 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H29ClN5O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.10M SPG (Succinic Acid, Sodium Dihydrogen Phosphate and Glycine) pH=4.00, 19.00 %w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.46→126.17 Å / Num. obs: 77008 / % possible obs: 94.7 % / Redundancy: 2.7 % / Rrim(I) all: 0.102 / Rsym value: 0.083 / Net I/σ(I): 11.15
Reflection shellResolution: 2.46→2.71 Å / Redundancy: 2.7 % / Num. unique obs: 19622 / Rrim(I) all: 0.534 / Rsym value: 0.439 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TVE

6tve


Resolution: 2.46→126.17 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.882 / SU B: 12.589 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.759 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.279 988 1.3 %RANDOM
Rwork0.2203 ---
obs0.221 76019 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.35 Å2 / Biso mean: 45.205 Å2 / Biso min: 14.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0.07 Å2
2--1.2 Å20 Å2
3----1.09 Å2
Refinement stepCycle: final / Resolution: 2.46→126.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16366 0 152 502 17020
Biso mean--40.97 34.76 -
Num. residues----2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916681
X-RAY DIFFRACTIONr_bond_other_d0.0030.0215666
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9722633
X-RAY DIFFRACTIONr_angle_other_deg1.246336011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3152103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71724.728717
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17215.0942770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1221571
X-RAY DIFFRACTIONr_chiral_restr0.0860.22542
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118922
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023675
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.02 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A12056
12B12056
21A12144
22C12144
31A12472
32D12472
41B12020
42C12020
51B12070
52D12070
61C12150
62D12150
LS refinement shellResolution: 2.46→2.524 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 78 -
Rwork0.332 5686 -
all-5764 -
obs--96.15 %

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