8TBB | pdb_00008tbb

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.241 (Depositor)
R-Value Work:
0.191 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TDQ0
Sequence Annotations Expand
Reference Sequence

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

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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	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D MOL2 format, chain D mmCIF format, chain D	D	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.241 (Depositor)
R-Value Work: 0.191 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2024-08-28
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.