7DUN | pdb_00007dun

Crystal structure of Fab fragment of Daratumumab

• PDB DOI: https://doi.org/10.2210/pdb7DUN/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• 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: 1.61 Å
• R-Value Free: 
  0.218 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Fab fragment of Daratumumab

Yu, X.J., Wang, L., Yu, C.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.77 kDa 
• Atom Count: 3,836 
• Modeled Residue Count: 432 
• Deposited Residue Count: 435 
• Unique protein chains: 2

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
Fab light chain	B [auth L]	212	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.218 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.905	α = 90
b = 89.905	β = 90
c = 217.477	γ = 120

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: 2024-11-13
  Changes: Structure summary