Experimental Data Snapshot
Starting Model:experimental
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(2009) Biophys J 97: 3178-3186
Nonsteroidal antiinflammatory drugs (NSAIDs), due to their good efficacy in the treatment of pain, inflammation, and fever, are among the most prescribed class of medicines in the world. The main drawback of NSAIDs is that they induce gastric complications such as peptic ulceration and injury to the intestine. Four NSAIDs, indomethacin, diclofenac, aspirin, and ibuprofen were selected to induce gastropathy in mouse models. It was found that the addition of C-terminal half of bovine lactoferrin (C-lobe) reversed the NSAID-induced injuries to the extent of 47-70% whereas the coadministration of C-lobe prevented it significantly. The C-lobe was prepared proteolytically using serine proteases. The binding studies of C-lobe with NSAIDs showed that these compounds bind to C-lobe with affinities ranging from 2.6 to 4.8 x 10(-4) M. The complexes of C-lobe were prepared with the above four NSAIDs. All four complexes were crystallized and their detailed three-dimensional structures were determined using x-ray crystallographic method. The structures showed that all the four NSAID molecules bound to C-lobe at the newly identified ligand binding site in C-lobe that is formed involving two alpha-helices, alpha10 and alpha11. The ligand binding site is separated from the well known iron binding site by the longest and the most stable beta-strand, betaj, in the structure. Similar results were also obtained with the full length lactoferrin molecule. This novel, to our knowledge, binding site in C-lobe of lactoferrin shows a good complementarity for the acidic and lipophilic compounds such as NSAIDs. We believe this indicates that C-lobe of lactoferrin can be exploited for the prevention of NSAID-induced gastropathy.
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (IMN)
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Lactotransferrin | 345 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P24627 | ||||
Glycosylation | |||||
| Glycosylation Sites: 3 | |||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| 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 | B | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G62783KT GlyCosmos:  G62783KT GlyGen:  G62783KT | |||||
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| IMN Query on IMN Download Ideal Coordinates CCD File  | J [auth A] | INDOMETHACIN C19 H16 Cl N O4 CGIGDMFJXJATDK-UHFFFAOYSA-N | |||
| NAG Query on NAG Download Ideal Coordinates CCD File  | I [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
| SO4 Query on SO4 Download Ideal Coordinates CCD File  | H [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
| ZN Query on ZN Download Ideal Coordinates CCD File  | D [auth A], E [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
| CO3 Query on CO3 Download Ideal Coordinates CCD File  | G [auth A] | CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L | |||
| FE Query on FE Download Ideal Coordinates CCD File  | F [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N | |||
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 63.839 | α = 90 |
| b = 50.654 | β = 107.56 |
| c = 66.119 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MAR345dtb | data collection |
| AMoRE | phasing |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational 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.