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- PDB-8p8c: HUMAN CD38 ECTODOMAIN BOUND TO COMPOUND 9-ADPR ADDUCT -

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Basic information

Entry
Database: PDB / ID: 8p8c
TitleHUMAN CD38 ECTODOMAIN BOUND TO COMPOUND 9-ADPR ADDUCT
ComponentsADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
KeywordsHYDROLASE / CD38 / NAD+ / NUCLEOPHILIC / COVALENT INHIBITOR
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of bone resorption / response to hydroperoxide ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of bone resorption / response to hydroperoxide / long-term synaptic depression / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / response to progesterone / female pregnancy / apoptotic signaling pathway / B cell receptor signaling pathway / positive regulation of insulin secretion / negative regulation of neuron projection development / response to estradiol / positive regulation of cytosolic calcium ion concentration / transferase activity / positive regulation of cell growth / basolateral plasma membrane / nuclear membrane / response to hypoxia / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase
Similarity search - Domain/homology
Chem-X5T / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 Å
AuthorsRangel, V. / Zebisch, M. / Doyle, K.J. / Burli, R.W.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Helv.Chim.Acta / Year: 2023
Title: A Covalent Binding Mode of a Pyrazole-Based CD38 Inhibitor
Authors: Doyle, K. / Roberts, M. / Harvey, J. / Hewer, R. / Zebisch, M. / Rangel, V. / Gu, M. / Wu, Y. / Yang, L. / Carlton, M. / Dawson, L. / Burli, R.
History
DepositionMay 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6142
Polymers29,6771
Non-polymers9381
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12630 Å2
Unit cell
Length a, b, c (Å)51.009, 61.464, 73.407
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / 2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose ...2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / 2'-phospho-cyclic-ADP-ribose transferase / ADP-ribosyl cyclase 1 / ADPRC 1 / Cyclic ADP-ribose hydrolase 1 / cADPR hydrolase 1 / T10


Mass: 29676.660 Da / Num. of mol.: 1 / Mutation: N100D, N164A, N209D, and N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZ alpha A / Production host: Komagataella pastoris (fungus)
References: UniProt: P28907, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase
#2: Chemical ChemComp-X5T / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[4-[4-[[4-(2-methoxyethoxy)cyclohexyl]amino]-1-methyl-2-oxidanylidene-quinolin-6-yl]pyrazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 937.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H49N9O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M bicine/NaOH pH 9.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.653→47.13 Å / Num. obs: 23165 / % possible obs: 81.8 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Rrim(I) all: 0.099 / Net I/σ(I): 10.4
Reflection shellResolution: 1.653→1.773 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1159 / CC1/2: 0.521 / Rpim(I) all: 0.533 / Rrim(I) all: 0.887 / % possible all: 21.9

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.653→47.13 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.148 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1195 -RANDOM
Rwork0.2024 ---
obs0.2045 23165 81.9 %-
Displacement parametersBiso mean: 26.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.1426 Å20 Å20 Å2
2--1.922 Å20 Å2
3----0.7793 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.653→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 64 171 2201
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012155HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.932980HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d766SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes352HARMONIC5
X-RAY DIFFRACTIONt_it2106HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion263SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2062SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion15.06
LS refinement shellResolution: 1.653→1.73 Å
RfactorNum. reflection% reflection
Rfree0.3078 24 -
Rwork0.3148 --
obs--13.33 %
Refinement TLS params.Origin x: 8.0395 Å / Origin y: 15.2994 Å / Origin z: 15.1747 Å
111213212223313233
T-0.0321 Å2-0.0019 Å20.0143 Å2-0.0053 Å2-0.003 Å2---0.0242 Å2
L0.3902 °2-0.0991 °20.3542 °2-0.2513 °2-0.1511 °2--0.6927 °2
S-0.0251 Å °0.0215 Å °-0.0396 Å °0.0215 Å °0.0085 Å °0.0079 Å °-0.0396 Å °0.0079 Å °0.0166 Å °
Refinement TLS groupSelection details: { A|* }

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