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- PDB-3roq: Crystal structure of human CD38 in complex with compound CZ-46 -

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Basic information

Entry
Database: PDB / ID: 3roq
TitleCrystal structure of human CD38 in complex with compound CZ-46
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CD38 / ADP-ribosyl cyclase / cyclic ADP-ribose / Calcium signaling / inhibitory compound / covalent intermediate / CZ-46 / HYDROLASE-HYDROLASE INHIBITOR complex
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 / long-term synaptic depression / negative regulation of bone resorption ...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 / long-term synaptic depression / negative regulation of bone resorption / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to hydroperoxide / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / apoptotic signaling pathway / response to progesterone / female pregnancy / 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; Chain A, domain 1 / ADP Ribosyl Cyclase; Chain A, domain 1 / ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase / NAD(P)-binding Rossmann-like Domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-46Z / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsZhang, H. / Lee, H.C. / Hao, Q.
CitationJournal: Biochemistry / Year: 2012
Title: Catalysis-based inhibitors of the calcium signaling function of CD38.
Authors: Kwong, A.K. / Chen, Z. / Zhang, H. / Leung, F.P. / Lam, C.M. / Ting, K.Y. / Zhang, L. / Hao, Q. / Zhang, L.H. / Lee, H.C.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references / Non-polymer description
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 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

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Assembly

Deposited unit
A: ADP-ribosyl cyclase 1
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7234
Polymers59,0792
Non-polymers6442
Water3,567198
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8622
Polymers29,5391
Non-polymers3221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8622
Polymers29,5391
Non-polymers3221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.881, 53.511, 63.906
Angle α, β, γ (deg.)109.330, 90.530, 94.830
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ADP-ribosyl cyclase 1 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / T10


Mass: 29539.479 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 45-296) / Mutation: N100D, N164D, N219D, N209D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P28907, NAD+ glycohydrolase
#2: Sugar ChemComp-46Z / (2R,3R,4S,5S)-4-fluoro-3,5-dihydroxytetrahydrofuran-2-yl 2-phenylethyl hydrogen (S)-phosphate / Inhibitor CZ-46 based on arabinosyl-2-fluoro-2-deoxynicotinamide mononucleotide, bound form


Type: D-saccharide, alpha linking / Mass: 322.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16FO7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE REAL LEAVING GROUP NICOTINAMIDE OF LIGAND 46Z CAN NOT BE SEEN IN THE STRUCTURE
Sequence detailsQ -> T AT THIS POSITION IN GENBANK AAA68482

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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: 2.28 Å3/Da / Density % sol: 46 % / Mosaicity: 1.521 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M sodium acetate pH4.0, 0.2M ammonium acetate, 3% isopropanol, 15% PEG 10000, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
51
61
71
81
91
101
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.063 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.063 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 37960 / % possible obs: 94.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.095 / Χ2: 1.34 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.91-1.982.50.54134511.002186.8
1.98-2.062.80.46637371.056293.1
2.06-2.1530.41438001.158395.5
2.15-2.263.30.35338551.317496.2
2.26-2.413.40.2938611.266596.5
2.41-2.593.50.20938811.27696.5
2.59-2.853.40.15638751.464797
2.85-3.273.30.09638871.579896.8
3.27-4.113.10.0638401.54995.9
4.11-502.90.05437731.5761094.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YH3

1yh3


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2678 / WRfactor Rwork: 0.2194 / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.7747 / SU B: 15.067 / SU ML: 0.183 / SU R Cruickshank DPI: 0.2994 / SU Rfree: 0.2273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 1482 5.1 %RANDOM
Rwork0.2157 ---
obs0.2183 29217 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 45.37 Å2 / Biso mean: 38.668 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--4.59 Å20.03 Å2-0.22 Å2
2--3.24 Å23.95 Å2
3---3.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 40 198 4300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224230
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9445743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3265503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10524.314204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15415730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1521526
X-RAY DIFFRACTIONr_chiral_restr0.0820.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213192
X-RAY DIFFRACTIONr_mcbond_it0.3851.52517
X-RAY DIFFRACTIONr_mcangle_it0.7224105
X-RAY DIFFRACTIONr_scbond_it1.34331713
X-RAY DIFFRACTIONr_scangle_it2.0434.51636
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 112 -
Rwork0.244 2018 -
all-2130 -
obs--95.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.205-0.4410.50283.5277-3.82578.1272-0.0555-0.17040.20220.0365-0.0838-0.1725-0.13520.42180.13930.2753-0.00130.01040.1498-0.11540.1311-389.763-918.4413.903
23.31251.6035-1.9872.9722-3.57458.315-0.09020.34070.5403-0.10240.028-0.0018-0.33-0.18630.06230.34090.02650.02290.1403-0.02870.2367-399.807-912.824.601
36.3698-0.75841.68011.6241-0.58247.7491-0.10250.06230.1703-0.08860.0113-0.36860.01870.55720.09120.382-0.01950.03340.2047-0.11390.1632-392.445-928.999-8.238
43.2210.50190.30870.9405-1.16646.0397-0.06470.0160.003-0.0663-0.01920.13360.10290.02120.08390.27230.02850.03730.0908-0.0970.1536-397.25-922.3639.658
54.6416-0.7696-0.29994.4403-1.03282.6929-0.1538-0.1731-0.48350.25640.05420.09750.3694-0.18890.09960.4806-0.05030.02890.2392-0.11930.1485-401.592-938.655-6.165
65.40670.8318-0.27964.35670.94634.4118-0.51720.8435-0.8855-0.31240.2439-0.80550.53650.47640.27330.5980.0230.13430.3611-0.14990.3302-389.694-939.399-14.724
75.5208-2.21950.49463.2554-0.65890.74110.29630.2114-1.0394-0.2322-0.08330.32010.181-0.0521-0.2130.3598-0.0077-0.04660.1894-0.14810.3224-414.454-947.98224.939
819.0711.4898-8.531217.3179-5.02235.46710.1454-0.3488-0.6970.918-0.25610.54430.1685-0.33620.11070.4410.00510.06170.25570.01240.1891-424.15-933.21834.444
911.2037-2.12811.78082.8267-1.47972.22070.2415-0.2694-0.80770.0708-0.1541-0.1828-0.10480.1509-0.08740.3188-0.0058-0.00070.1601-0.0780.2267-407.333-945.06628.808
102.95050.57380.13663.75340.27354.16340.0503-0.20780.13010.2981-0.0194-0.2243-0.09670.1893-0.0310.32260.00150.02680.1505-0.0960.0878-416.089-922.04729.076
1129.4829.4674-18.85164.3206-6.079812.6219-0.0704-0.8401-0.35690.4015-0.15190.24740.20710.19470.22240.5330.0560.02630.3601-0.08010.2324-430.44-922.61640.386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 70
2X-RAY DIFFRACTION2A71 - 115
3X-RAY DIFFRACTION3A116 - 140
4X-RAY DIFFRACTION4A141 - 193
5X-RAY DIFFRACTION5A194 - 268
6X-RAY DIFFRACTION6A269 - 296
7X-RAY DIFFRACTION7B45 - 123
8X-RAY DIFFRACTION8B124 - 144
9X-RAY DIFFRACTION9B145 - 193
10X-RAY DIFFRACTION10B194 - 271
11X-RAY DIFFRACTION11B272 - 296

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