9I1Q | pdb_00009i1q

HER3 receptor in complex with the Fab fragment of TK-hu A3 monoclonal antibody

PDB DOI: https://doi.org/10.2210/pdb9I1Q/pdb

Classification: ANTITUMOR PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens, Cricetulus griseus
Mutation(s): No

Deposited: 2025-01-16 Released: 2025-10-15
Deposition Author(s): Bulfaro, G., Savino, C., Costanzo, A., Fata, F., Vallone, B., Montemiglio, L.C.
Funding Organization(s): Regione Lazio (Italy)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.263 (Depositor), 0.258 (DCC)
R-Value Work:
0.209 (Depositor), 0.208 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Models: in silico, experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Novel Humanized Anti-HER3 Antibodies: Structural Characterization and Therapeutic Activity

Muzi, A., Arriga, R., Bulfaro, G., Fata, F., Costanzo, A., Chiarini, V., Cappelletti, M., Ferrara, F.F., Bucci, F., Montemiglio, L.C., Savino, C., Marra, E., Ciliberto, G., Aurisicchio, L., Vallone, B., Roscilli, G.

(2025) Antibodies (Basel) 14

DOI: https://doi.org/10.3390/antib14040084

Macromolecule Content

Total Structure Weight: 481 kDa
Atom Count: 31,872
Modeled Residue Count: 4,062
Deposited Residue Count: 4,300
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-3	A, B, C, D	632	Homo sapiens	Mutation(s): 0 Gene Names: ERBB3, HER3 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21860 (Homo sapiens) Explore P21860 Go to UniProtKB: P21860
PHAROS: P21860 GTEx: ENSG00000065361
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21860
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P21860-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain hA3-Fab	E, F, G, H	220	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain hA3-Fab	I, J, K, L	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, O	3		N-Glycosylation	Interactions Focus chain M Focus chain O Interactions & Density Focus chain M Focus chain O

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N	4		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P, Q	2		N-Glycosylation	Interactions Focus chain P Focus chain Q Interactions & Density Focus chain P Focus chain Q

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] EA [auth C] FA [auth C] AA [auth B], BA [auth B], CA [auth B], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], KA [auth D], LA [auth D], MA [auth D], NA [auth D], OA [auth D], PA [auth D], QA [auth D], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain JA [auth C] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth H] SDF format, chain UA [auth H] SDF format, chain VA [auth I] SDF format, chain WA [auth I] SDF format, chain XA [auth L] MOL2 format, chain DA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth H] MOL2 format, chain UA [auth H] MOL2 format, chain VA [auth I] MOL2 format, chain WA [auth I] MOL2 format, chain XA [auth L] mmCIF format, chain DA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth H] mmCIF format, chain UA [auth H] mmCIF format, chain VA [auth I] mmCIF format, chain WA [auth I] mmCIF format, chain XA [auth L]	DA [auth B] JA [auth C] RA [auth D] SA [auth D] TA [auth H] DA [auth B], JA [auth C], RA [auth D], SA [auth D], TA [auth H], UA [auth H], VA [auth I], WA [auth I], XA [auth L]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain JA [auth C] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain VA [auth I] Focus chain WA [auth I] Focus chain XA [auth L] Interactions & Density Focus chain DA [auth B] Focus chain JA [auth C] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain VA [auth I] Focus chain WA [auth I] Focus chain XA [auth L]