9I6Q | pdb_00009i6q

Structure of Fab-Fragment GB11 agains tumour associated carbohydrate antigens.

PDB DOI: https://doi.org/10.2210/pdb9I6Q/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2025-01-31 Released: 2026-02-18
Deposition Author(s): Freitag, A., Khilji, S.K., Nedielkov, R., Kumar, S.M., Krummhaar, M., Luehle, J., Goerdeler, F., Arndt, J., Kamphues, C., Mroginski, M.A., Roth, C., Seeberger, P.H., Moeller, H.M., Moscovitz, O.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.239 (Depositor), 0.238 (DCC)
R-Value Work:
0.200 (Depositor), 0.199 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Integrative Approach to Develop and Characterize Antibodies against the Cancer-Associated Antigen Sialyl Lewis A (CA 19-9).

Freitag, A., Khilji, S.K., Nedielkov, R., M Kumar, S., Krummhaar, M., Arndt, J., Moreira, G.M.S.G., Luhle, J., Goerdeler, F., Kamphues, C., Mroginski, M.A., Roth, C., Seeberger, P.H., Moller, H.M., Moscovitz, O.

(2026) JACS Au 6: 2274-2287

PubMed: 42063835 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacsau.5c01596
Primary Citation Related Structures:
9I6Q, 9I9H

PubMed Abstract:
Sialyl Lewis A (sLeA), or the CA 19-9 marker, is the best validated and only FDA-approved serologic marker clinically used to monitor recurrence, progression, and therapy efficiency in pancreatic ductal adenocarcinoma (PDAC) patients, making it an attractive target for antibody development. Recent clinical trials have demonstrated satisfying safety profiles and unique expression in a range of malignancies that highlight CA 19-9 as an attractive TACA to target using a stand-alone drug or an adjuvant therapy. Hence, we set out to explore the use of synthetic sLeA in the development of additional monoclonal antibodies (mAbs) with enhanced sLeA recognition and improved efficacy. Two mAbs targeting sLeA were generated through mice immunization with synthetic sLeA glycoconjugates, synthetic glycan arrays, and hybridoma technology. We then compared the antigen-binding properties of the newly developed mAbs with those of the widely used mAb 1116-NS-19-9 and demonstrated improved affinity and specificity for native sLeA ectopically expressed in B16 melanoma cells, surpassing the performance of the established mAb 1116-NS-19-9. Of the two mAbs, GB11 was more promising. Therefore, to elucidate the structural origin of improved GB11's antigen binding, we conducted high-resolution mapping of the molecular recognition patterns between sLeA and the different antibodies using X-ray crystallography and STD NMR. These analyses revealed subtle yet critical differences in the glycan engagement and identified key structural features underlying enhanced GB11's recognition of sLeA. MD simulations further supported these observations, indicating distinct orientations of sLeA within the binding pockets of each mAb. Our results suggest improved recognition of the native sLeA antigen by the newly generated GB11 antibody, providing a detailed and high-resolution elucidation of the molecular interactions underlying this recognition. Our study provides a tool with improved theranostic properties against sLeA-overexpressing malignancies.

Organizational Affiliation

Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany.

Macromolecule Content

Total Structure Weight: 55.79 kDa
Atom Count: 3,644
Modeled Residue Count: 429
Deposited Residue Count: 491
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain	A [auth H]	277	Mus musculus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment variable chain	B [auth L]	214	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain E [auth H] SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain P [auth H] SDF format, chain Q [auth L] SDF format, chain R [auth L] SDF format, chain S [auth L] SDF format, chain T [auth L] SDF format, chain U [auth L] SDF format, chain V [auth L] SDF format, chain W [auth L] MOL2 format, chain C [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth L] MOL2 format, chain S [auth L] MOL2 format, chain T [auth L] MOL2 format, chain U [auth L] MOL2 format, chain V [auth L] MOL2 format, chain W [auth L] mmCIF format, chain C [auth H] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth L] mmCIF format, chain R [auth L] mmCIF format, chain S [auth L] mmCIF format, chain T [auth L] mmCIF format, chain U [auth L] mmCIF format, chain V [auth L] mmCIF format, chain W [auth L]	C [auth H] E [auth H] F [auth H] G [auth H] H C [auth H], E [auth H], F [auth H], G [auth H], H, I [auth H], J [auth H], K [auth H], L [auth H], M [auth H], N [auth H], O [auth H], P [auth H], Q [auth L], R [auth L], S [auth L], T [auth L], U [auth L], V [auth L], W [auth L]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth L] Focus chain V [auth L] Focus chain W [auth L] Interactions & Density Focus chain C [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth L] Focus chain V [auth L] Focus chain W [auth L]