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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.271 (Depositor), 0.234 (DCC)
R-Value Work:
0.244 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8TFT

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., 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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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

Find similar proteins by:

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

Find similar proteins by:

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

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 H [auth G] SDF format, chain G [auth F] MOL2 format, chain H [auth G] MOL2 format, chain G [auth F] mmCIF format, chain H [auth G] mmCIF format, chain G [auth F]	G [auth F], H [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth F] Focus chain H [auth G] Interactions & Density Focus chain G [auth F] Focus chain H [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.271 (Depositor), 0.234 (DCC)
R-Value Work: 0.244 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Oganesyan, V.Y.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.