[English] 日本語
Yorodumi
- PDB-7jv8: Human CD73 (ecto 5'-nucleotidase) in complex with compound 35 -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / AMP catabolic process ...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 / AMP catabolic process / GMP 5'-nucleotidase activity / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Nicotinate metabolism / Purine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / DNA metabolic process / leukocyte cell-cell adhesion / response to ATP / response to inorganic substance / calcium ion homeostasis / Purinergic signaling in leishmaniasis infection / ATP metabolic process / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / extracellular exosome / zinc ion binding / nucleoplasm / membrane / identical protein binding / 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
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

-
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)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: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0

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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
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