+Open data
-Basic information
Entry | Database: PDB / ID: 8byu | ||||||
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Title | Crystal Structure of HexaBody-CD38 Fab in complex with CD38 | ||||||
Components |
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Keywords | ANTITUMOR PROTEIN / CD38 / Antibody / CDC / HexaBody / Anti-Tumor | ||||||
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 / 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 / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / 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 / response to estradiol / negative regulation of neuron projection development / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Freier, R. / Krapp, S. / Hibbert, R.G. | ||||||
Funding support | 1items
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Citation | Journal: Ebiomedicine / Year: 2023 Title: Preclinical anti-tumour activity of HexaBody-CD38, a next-generation CD38 antibody with superior complement-dependent cytotoxic activity. Authors: Hiemstra, I.H. / Santegoets, K.C.M. / Janmaat, M.L. / De Goeij, B.E.C.G. / Ten Hagen, W. / van Dooremalen, S. / Boross, P. / van den Brakel, J. / Bosgra, S. / Andringa, G. / van Kessel- ...Authors: Hiemstra, I.H. / Santegoets, K.C.M. / Janmaat, M.L. / De Goeij, B.E.C.G. / Ten Hagen, W. / van Dooremalen, S. / Boross, P. / van den Brakel, J. / Bosgra, S. / Andringa, G. / van Kessel-Welmers, B. / Verzijl, D. / Hibbert, R.G. / Frerichs, K.A. / Mutis, T. / van de Donk, N.W.C.J. / Ahmadi, T. / Satijn, D. / Sasser, A.K. / Breij, E.C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8byu.cif.gz | 171.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8byu.ent.gz | 131.7 KB | Display | PDB format |
PDBx/mmJSON format | 8byu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/8byu ftp://data.pdbj.org/pub/pdb/validation_reports/by/8byu | HTTPS FTP |
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-Related structure data
Related structure data | 1yh3S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 30478.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 25112.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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#2: Antibody | Mass: 23383.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
-Non-polymers , 4 types, 626 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.99 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.15 M (NH4)2SO4; 0.1 M HEPES: pH:7.0; 20.0 %w/v PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.848→61 Å / Num. obs: 63099 / % possible obs: 98.7 % / Redundancy: 3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.126 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.848→1.88 Å / Num. unique obs: 2880 / CC1/2: 0.589 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YH3 Resolution: 1.85→61 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.036 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.405 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→61 Å
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