8TFT | pdb_00008tft

Fab of O13-1 human IgG1 antibody bound to IgV domain of human TIM-3

• PDB DOI: https://doi.org/10.2210/pdb8TFT/pdb

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


• Deposited: 2023-07-11 Released: 2024-08-28 
• Deposition Author(s): Oganesyan, V.Y., van Dyk, N., Mazor, Y., Yang, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.250 (DCC) 

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., Moynihan, J., van Dyk, N., Yang, C., Garcia, A., Yu, J., Miller, C., Mulgrew, K., Cobbold, M., Mazor, Y., Hammond, S.A., Pollizzi, K.N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 118.77 kDa 
• Atom Count: 8,313 
• Modelled Residue Count: 1,090 
• Deposited Residue Count: 1,098 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-13-1 IgG1 Fab heavy chain	A [auth I], D [auth H]	227	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
O-13-1 IgG1 Fab light chain	B [auth M], E [auth L]	213	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell immunoglobulin mucin receptor 3	C [auth F], F [auth G]	109	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth F], H [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.250 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.338	α = 90
b = 69.785	β = 99.897
c = 93.632	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.Y., van Dyk, N., Mazor, Y., Yang, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Structure summary