3IAZ

Structural basis of the prevention of NSAID-induced damage of the gastrointestinal tract by C-terminal half (C-lobe) of bovine colostrum protein lactoferrin: Binding and structural studies of the C-lobe complex with aspirin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

The structural basis for the prevention of nonsteroidal antiinflammatory drug-induced gastrointestinal tract damage by the C-lobe of bovine colostrum lactoferrin

Mir, R.Singh, N.Vikram, G.Kumar, R.P.Sinha, M.Bhushan, A.Kaur, P.Srinivasan, A.Sharma, S.Singh, T.P.

(2009) Biophys J 97: 3178-3186

  • DOI: 10.1016/j.bpj.2009.09.030
  • Primary Citation of Related Structures:  
    3IAZ, 3IB0, 3IB1, 3IB2

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LactotransferrinA345Bos taurusMutation(s): 0 
Gene Names: LTF
EC: 3.4.21
UniProt
Find proteins for P24627 (Bos taurus)
Explore P24627 
Go to UniProtKB:  P24627
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G99907OV
GlyCosmos:  G99907OV
GlyGen:  G99907OV
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05674CR
GlyCosmos:  G05674CR
GlyGen:  G05674CR
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AIN (Subject of Investigation/LOI)
Query on AIN

Download Ideal Coordinates CCD File 
E [auth A]2-(ACETYLOXY)BENZOIC ACID
C9 H8 O4
BSYNRYMUTXBXSQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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G [auth A], H [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

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J [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

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I [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download Ideal Coordinates CCD File 
K [auth A]ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AIN Binding MOAD:  3IAZ Kd: 3.30e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.308α = 90
b = 50.469β = 107.7
c = 65.942γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2018-08-01
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2018-08-15
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary