9YZZ | pdb_00009yzz

Crystal structure of Trastuzumab Fab conjugated to Linker-Payload

• PDB DOI: https://doi.org/10.2210/pdb9YZZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2025-10-30 Released: 2025-12-24 
• Deposition Author(s): Jaime-Garza, M., Noland, C.L., Gabelli, S.B.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.289 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

Structural Characterization of Linker Shielding in ADC Site-Specific Conjugates

Jaime-Garza, M., Waight, A., Hudlikar, M., Eddins, M.J., Rasti, E.S., Zaragoza, J.P.T., Fayadat-Dilman, L., Chrencik, J.E., Gabelli, S.B., Chen, Y.T., Noland, C.L.

(2025) Pharmaceutics 17: 1568

• DOI: https://doi.org/10.3390/pharmaceutics17121568

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: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 52.75 kDa 
• Atom Count: 3,221 
• Modeled Residue Count: 421 
• Deposited Residue Count: 477 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trastuzumab Light Chain	A [auth L]	233	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trastuzumab Heavy Chain	B [auth H]	244	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CZS (Subject of Investigation/LOI)	D [auth H]	N-({[4-({N-[3-(2,5-dioxopyrrolidin-1-yl)propanoyl]-L-alanyl-L-alanyl}amino)phenyl]methoxy}carbonyl)-N-methyl-L-valyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide C60 H91 N9 O14 FQLMLVWEYZJWED-KUVRQIMGSA-N
CO	C [auth L], E [auth H]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.289 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.902	α = 90
b = 64.941	β = 129.905
c = 83.81	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
pointless	data scaling
Aimless	data scaling
PHENIX	refinement
Coot	model building
STARANISO	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Jaime-Garza, M., Noland, C.L., Gabelli, S.B.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release