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- PDB-3rop: Crystal structure of human CD38 in complex with compound CZ-50b -

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Basic information

Entry
Database: PDB / ID: 3rop
TitleCrystal structure of human CD38 in complex with compound CZ-50b
ComponentsADP-ribosyl cyclase 1Cyclic ADP-ribose
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CD38 / ADP-ribosyl cyclase / cyclic ADP-ribose / X-crystallography / Calcium signaling / inhibitory compound / covalent intermediate / CZ-50b / 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 / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / 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 / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / 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 / 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 / membrane / identical protein binding / 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-50A / NICOTINAMIDE / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 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 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references / Non-polymer description
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / software / 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 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)59,7876
Polymers59,0792
Non-polymers7084
Water4,792266
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8943
Polymers29,5391
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8943
Polymers29,5391
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.817, 53.630, 63.540
Angle α, β, γ (deg.)109.72, 91.19, 94.81
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ADP-ribosyl cyclase 1 / Cyclic ADP-ribose / 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-50A / 2-deoxy-2-fluoro-5-O-phosphono-alpha-D-ribofuranose / Inhibitor CZ-50b arabinosyl-2-fluoro-2-deoxynicotinamide mononucleotide, bound form / 2-deoxy-2-fluoro-5-O-phosphono-alpha-D-ribose / 2-deoxy-2-fluoro-5-O-phosphono-D-ribose / 2-deoxy-2-fluoro-5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 232.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10FO7P
IdentifierTypeProgram
D-1-deoxy-Ribf2fluoro5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE REAL LEAVING GROUP NICOTINAMIDE OF LIGAND 50A 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: 2.26 Å3/Da / Density % sol: 45.56 % / Mosaicity: 0.798 °
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97908 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 37381 / % possible obs: 97.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Χ2: 1.428 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.94-2.023.70.33936860.827196.6
2.02-2.13.70.25637400.871196.8
2.1-2.23.70.20737330.98197.4
2.2-2.313.70.16637021.132197.4
2.31-2.463.70.13837571.097197.7
2.46-2.653.70.11337481.327198.1
2.65-2.913.80.09937361.477198.3
2.91-3.333.70.08737901.912198.6
3.33-4.23.60.07437922.294198.8
4.2-503.50.06836972.417197.1

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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: 1.94→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.1801 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8758 / SU B: 7.537 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1707 / SU Rfree: 0.1465 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.20834 1891 5.1 %RANDOM
Rwork0.17284 ---
obs0.17462 35482 96.77 %-
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: 58.64 Å2 / Biso mean: 34.627 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20.07 Å20.51 Å2
2--2.38 Å20.33 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 44 266 4396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224245
X-RAY DIFFRACTIONr_bond_other_d0.0010.022924
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9455756
X-RAY DIFFRACTIONr_angle_other_deg0.82737102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26424.175206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39815736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6721528
X-RAY DIFFRACTIONr_chiral_restr0.0720.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214652
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02874
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5381.52520
X-RAY DIFFRACTIONr_mcbond_other0.1361.51002
X-RAY DIFFRACTIONr_mcangle_it1.08424108
X-RAY DIFFRACTIONr_scbond_it1.81531725
X-RAY DIFFRACTIONr_scangle_it2.9124.51648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.935→1.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 111 -
Rwork0.211 2358 -
obs--84.76 %
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)
155.5756-50.309968.405245.5565-61.928884.20691.14870.7391-0.2822-1.0707-0.77140.14741.52030.9941-0.37740.47410.2811-0.19950.7020.25510.912211.065-9.49260.308
217.2127-2.12354.79996.9613-1.96874.29010.6293-0.1683-1.5523-0.15940.00610.66340.4801-0.5322-0.63540.1743-0.0228-0.04040.1316-0.01580.4619-16.697-9.11650.812
35.0721-2.4050.56073.56550.10470.68870.38641.0063-1.1222-0.4442-0.21760.2260.16030.1613-0.16880.17530.0712-0.0440.2867-0.19930.3419-7.657-3.10843.378
413.46234.914-3.74548.5097-1.51645.2180.2481-0.3635-0.16540.5494-0.14050.5410.2784-0.1862-0.10750.1930.05220.04590.10980.01640.0681-17.4598.73458.265
56.63-2.54641.2843.8795-1.28051.60880.13920.0725-0.723-0.0259-0.1428-0.16940.0810.26230.00360.0970.0029-0.01630.0784-0.01370.1725-2.879-0.41950.299
63.5293-0.05-1.45982.4630.52423.08760.0465-0.39450.1860.31630.04050.073-0.15690.0927-0.08710.13640.02-0.01340.09820.00620.0676-13.18520.94157.319
72.17460.1645-0.86623.8406-4.097610.0173-0.0192-0.18160.04970.1265-0.2054-0.2363-0.40090.58390.22450.0419-0.0004-0.03110.0630.00120.08816.99724.49335.495
83.07071.5728-3.28192.7689-2.88068.80220.12080.23630.2977-0.08880.02830.0804-0.3549-0.2709-0.1490.11570.0668-0.00180.05450.03590.10885.7529.60329.081
910.3931-0.32280.30496.3825-1.25594.1561-0.25740.5040.0777-0.22090.0324-0.55840.12240.41440.2250.1877-0.03160.02080.1385-0.06180.132814.53413.38815.254
103.99981.1795-0.80161.3265-0.95286.6225-0.0191-0.2939-0.2269-0.0143-0.08130.02390.0994-0.09820.10040.04230.0183-0.01570.03610.01270.06569.01919.97835.441
114.9459-1.13510.01775.5008-0.06425.8833-0.3355-0.0861-0.20820.14780.24020.23070.2388-0.44490.09530.1425-0.09110.01920.1131-0.01990.09883.2078.94718.777
126.4681-2.36750.52613.37130.35181.482-0.06040.3459-0.1393-0.170.0165-0.18750.21170.1290.0440.3327-0.01850.04290.1527-0.06080.215712.296-0.3912.529
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 55
2X-RAY DIFFRACTION2A56 - 79
3X-RAY DIFFRACTION3A80 - 124
4X-RAY DIFFRACTION4A125 - 143
5X-RAY DIFFRACTION5A144 - 203
6X-RAY DIFFRACTION6A204 - 296
7X-RAY DIFFRACTION7B45 - 75
8X-RAY DIFFRACTION8B76 - 116
9X-RAY DIFFRACTION9B117 - 144
10X-RAY DIFFRACTION10B145 - 192
11X-RAY DIFFRACTION11B193 - 237
12X-RAY DIFFRACTION12B238 - 296

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