8BYU

Crystal Structure of HexaBody-CD38 Fab in complex with CD38

• PDB DOI: https://doi.org/10.2210/pdb8BYU/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2022-12-14 Released: 2023-07-12 
• Deposition Author(s): Freier, R., Krapp, S., Hibbert, R.G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Preclinical anti-tumour activity of HexaBody-CD38, a next-generation CD38 antibody with superior complement-dependent cytotoxic activity.

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.

(2023) EBioMedicine 93: 104663-104663

• PubMed: 37379657 
• DOI: https://doi.org/10.1016/j.ebiom.2023.104663
• Primary Citation of Related Structures:  
  8BYU


• PubMed Abstract: 
  

  HexaBody®-CD38 (GEN3014) is a hexamerization-enhanced human IgG1 that binds CD38 with high affinity. The E430G mutation in its Fc domain facilitates the natural process of antibody hexamer formation upon binding to the cell surface, resulting in increased binding of C1q and potentiated complement-dependent cytotoxicity (CDC).

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Organizational Affiliation: 

Genmab B.V., Utrecht, the Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 79.57 kDa 
• Atom Count: 6,308 
• Modelled Residue Count: 684 
• Deposited Residue Count: 711 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Heavy Chain	A [auth H]	235	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Light Chain	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1	C [auth A]	262	Homo sapiens	Mutation(s): 0  Gene Names: CD38 EC: 3.2.2.6 (PDB Primary Data), 2.4.99.20 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P28907 (Homo sapiens) Explore P28907  Go to UniProtKB:  P28907
PHAROS:  P28907 GTEx:  ENSG00000004468

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth H], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth H], F [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.24	α = 90
b = 78.309	β = 91.94
c = 98.162	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Freier, R., Krapp, S., Hibbert, R.G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description