[English] 日本語
Yorodumi
- PDB-9hjg: Crystal structure of human CD73 (ecto-5'-nucleotidase) in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hjg
TitleCrystal structure of human CD73 (ecto-5'-nucleotidase) in complex with an N6-disubstituted acyclic ADP analog (compound 26 in publication) in the closed state
Components5'-nucleotidase
KeywordsHYDROLASE / nucleotide analog / dimetal center / closed state
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, 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 / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsStrater, N. / Moschuetz, S. / Federico, S. / Renn, C. / Muller, C.E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)335447717 Germany
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Acyclic purine and pyrimidine nucleotide analogs as ecto-5'-nucleotidase (CD73) inhibitors.
Authors: Federico, S. / Renn, C. / Brehova, P. / Janeba, Z. / Moschutz, S. / Sylvester, K. / Shamleh, R.A. / Baburi, H. / Zimmermann, H. / El-Tayeb, A. / Strater, N. / Muller, C.E.
History
DepositionNov 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)244,32719
Polymers241,6224
Non-polymers2,70615
Water00
1
A: 5'-nucleotidase
B: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1449
Polymers120,8112
Non-polymers1,3337
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-112 kcal/mol
Surface area40010 Å2
2
C: 5'-nucleotidase
D: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,18410
Polymers120,8112
Non-polymers1,3738
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-122 kcal/mol
Surface area39760 Å2
Unit cell
Length a, b, c (Å)93.593, 84.551, 124.667
Angle α, β, γ (deg.)90.00, 102.62, 90.00
Int Tables number4
Space group name H-MP1211

-
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: 60405.418 Da / Num. of mol.: 4
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, 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.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-A1IVH / [5-[2-chloranyl-6-[methyl-(phenylmethyl)amino]purin-9-yl]pentoxy-oxidanyl-phosphoryl]methylphosphonic acid


Mass: 517.840 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H26ClN5O6P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 6000 and 0.1 M Hepes pH 7.0, 10 microM ZnCl2, 10 mM inhibitor and 10 % PEG 200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.31→121.66 Å / Num. obs: 36814 / % possible obs: 83.5 % / Redundancy: 6 % / Biso Wilson estimate: 26.4 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.364 / Rpim(I) all: 0.161 / Rrim(I) all: 0.399 / Net I/σ(I): 4.6
Reflection shellResolution: 2.31→2.67 Å / Rmerge(I) obs: 1.018 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1773 / CC1/2: 0.697 / Rpim(I) all: 0.453 / Rrim(I) all: 1.116

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→121.66 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2711 1777 4.83 %
Rwork0.2368 --
obs0.2385 36783 44.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→121.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16262 0 143 0 16405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616764
X-RAY DIFFRACTIONf_angle_d0.8122713
X-RAY DIFFRACTIONf_dihedral_angle_d12.9696271
X-RAY DIFFRACTIONf_chiral_restr0.0512508
X-RAY DIFFRACTIONf_plane_restr0.0072959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.380490.3335198X-RAY DIFFRACTION3
2.37-2.440.4581140.3314268X-RAY DIFFRACTION5
2.44-2.520.2978210.3133374X-RAY DIFFRACTION6
2.52-2.610.3944270.3134481X-RAY DIFFRACTION8
2.61-2.720.4454310.3438692X-RAY DIFFRACTION11
2.72-2.840.3104550.31661196X-RAY DIFFRACTION20
2.84-2.990.3444920.31251873X-RAY DIFFRACTION31
2.99-3.180.34991630.30192979X-RAY DIFFRACTION49
3.18-3.420.34012410.28724495X-RAY DIFFRACTION74
3.42-3.770.3032240.25974562X-RAY DIFFRACTION74
3.77-4.310.27772770.22115584X-RAY DIFFRACTION91
4.31-5.430.20473310.19326083X-RAY DIFFRACTION99
5.43-121.660.23012920.2056221X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more