9XXU | pdb_00009xxu

Crystal structure of the chymotrypsin-cleaved iron-free C-lobe of bovine lactoferrin at 2.82 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb9XXU/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2025-12-01 Released: 2025-12-31
Deposition Author(s): Pandit, S., Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.211 (Depositor), 0.216 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Basis for Single-Site Cleavage of Lactoferrin by Diverse Proteases for Prolonged Antibacterial Action: Structure of the Chymotrypsin-Cleaved Lactoferrin C-Lobe.

Pandit, S., Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.

(2026) Proteins

PubMed: 42230792 Search on PubMed
DOI: https://doi.org/10.1002/prot.70148
Primary Citation Related Structures:
9XXU

PubMed Abstract:
The stable lactoferrin C-lobe offers strong potential for therapeutic applications as an antibacterial agent. Lactoferrin is a 78 kDa (Ala1Arg689) iron-binding glycoprotein which is composed of two homologous N- and C-lobes, connected by an 11-residue α-helical linker (Thr334Arg344). The limited proteolysis of lactoferrin, carried out using chymotrypsin, generated a 40 kDa, fully functional C-lobe. The structure determination revealed that the protein chain consisted of residues from Thr343 to Leu680 together with a disulfide-linked tripeptide, Ala683Cys684Ala685. It showed that the cleavage occurred specifically at the Tyr342Thr343 peptide bond within the inter-lobe 11-residue-long peptide. Remarkably, previous studies using proteinase K, trypsin, and pepsin also produced an identical C-lobe. Thus, the inter-lobe region seems to be stereochemically designed by nature for the single-site cleavage by multiple digestive enzymes. The proteolytically generated C-lobe, with three observed glycosylation sites, remains stable for 3 days in the presence of digestive enzymes. The stable C-lobe continues to sequester iron, thus showing a prolonged antibacterial property. This is a unique example of evolutionary convergence whereby multiple digestive enzymes cleave a native protein into a stable half molecule with full antibacterial action.

Organizational Affiliation

Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.

Macromolecule Content

Total Structure Weight: 80.8 kDa
Atom Count: 5,564
Modeled Residue Count: 682
Deposited Residue Count: 694
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactotransferrin	A, C [auth B]	338	Bos taurus	Mutation(s): 0 EC: 3.4.21
UniProt
Find proteins for P24627 (Bos taurus) Explore P24627 Go to UniProtKB: P24627
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24627
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain C [auth B]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal fragment of Lactotransferrin	B [auth C], D	9	Bos taurus	Mutation(s): 0 EC: 3.4.21
UniProt
Find proteins for P24627 (Bos taurus) Explore P24627 Go to UniProtKB: P24627
Entity Groups
UniProt Group	P24627
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[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	E, H	5		N-Glycosylation	Interactions Focus chain E Focus chain H Interactions & Density Focus chain E Focus chain H
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	F, G	6		N-Glycosylation	Interactions Focus chain F Focus chain G Interactions & Density Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B]	M [auth A], Q [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain Q [auth B] Interactions & Density Focus chain M [auth A] Focus chain Q [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B]	N [auth A], O [auth A], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B]	J [auth A], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A]	I [auth A], L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth A] Interactions & Density Focus chain I [auth A] Focus chain L [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]