8TBB

F9S, novel TIM-3 targeting antibody, bound to IgV domain of TIM-3

• PDB DOI: https://doi.org/10.2210/pdb8TBB/pdb

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


• Deposited: 2023-06-28 Released: 2024-08-28 
• Deposition Author(s): Oganesyan, V., van Dyk, N., Mazor, Y., Yang, C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.241 
• R-Value Work: 0.191 

Starting Model: experimental

Literature

Generation of AZD7789, a novel PD-1 and TIM-3 targeting bispecific antibody, which binds to a differentiated epitope of TIM-3

Clancy-Thompson, E., Perry, T., Pryts, S., Jaiswal, A., Oganesyan, V., van Dyk, N., Yang, C., Garcia, A., Yu, W., Moynihan, J., Miller, C., Mulgrew, K., Cobbold, M., Mazor, Y., Hammond, S., Pollizzi, K.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 60.06 kDa 
• Atom Count: 4,315 
• Modelled Residue Count: 541 
• Deposited Residue Count: 550 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell immunoglobulin mucin receptor 3	A [auth D]	110	Homo sapiens	Mutation(s): 0  Gene Names: HAVCR2, TIM3, TIMD3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDQ0 (Homo sapiens) Explore Q8TDQ0  Go to UniProtKB:  Q8TDQ0
PHAROS:  Q8TDQ0 GTEx:  ENSG00000135077

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F9S Fab heavy chain	B [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
F9S Fab light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.241 
• R-Value Work: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.805	α = 90
b = 57.005	β = 106
c = 80.453	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Oganesyan, V., van Dyk, N., Mazor, Y., Yang, C.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release