7DUO | pdb_00007duo

Crystal structure of daratumumab fab and CD38 complex

• PDB DOI: https://doi.org/10.2210/pdb7DUO/pdb

• Classification: ANTITUMOR PROTEIN/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Mammalian expression vector BsrGI-MCS-pcDNA3.1
• Mutation(s): No 


• Deposited: 2021-01-10 Released: 2021-03-10 
• Deposition Author(s): Yu, X.J., Wang, L., Yu, C.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 

Starting Model: experimental

Literature

Crystal structure of daratumumab fab and CD38 complex

Yu, X.J., Wang, L., Yu, C.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 73.55 kDa 
• Atom Count: 5,085 
• Modeled Residue Count: 652 
• Deposited Residue Count: 665 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	A [auth H]	223	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1	B	229	Homo sapiens	Mutation(s): 0  Gene Names: CD38 EC: 3.2.2.6 (PDB Primary Data), 2.4.99.20 (PDB Primary Data), 3.2.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P28907 (Homo sapiens) Explore P28907  Go to UniProtKB:  P28907
PHAROS:  P28907 GTEx:  ENSG00000004468

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	C [auth L]	213	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.611	α = 90
b = 54.658	β = 98.16
c = 93.052	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Yu, X.J., Wang, L., Yu, C.F.

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary