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- PDB-1xv4: Solution structure of antimicrobial and endotoxin-neutralizing pe... -

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Basic information

Entry
Database: PDB / ID: 1xv4
TitleSolution structure of antimicrobial and endotoxin-neutralizing peptide Lf11 in SDS micelles
Componentslactoferrin-based synthetic peptide FQWQRNIRKVR
KeywordsMETAL TRANSPORT / loop / hydrophobic core
Function / homology
Function and homology information


negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism ...negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of osteoclast development / specific granule / antifungal humoral response / negative regulation of ATP-dependent activity / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / cysteine-type endopeptidase inhibitor activity / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / humoral immune response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / protein serine/threonine kinase activator activity / secretory granule / innate immune response in mucosa / lipopolysaccharide binding / positive regulation of protein serine/threonine kinase activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / antibacterial humoral response / positive regulation of NF-kappaB transcription factor activity / heparin binding / iron ion transport / defense response to Gram-negative bacterium / positive regulation of canonical NF-kappaB signal transduction / killing of cells of another organism / early endosome / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsJapelj, B. / Pristovsek, P. / Majerle, A. / Jerala, R.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural origin of endotoxin neutralization and antimicrobial activity of a lactoferrin-based peptide
Authors: Japelj, B. / Pristovsek, P. / Majerle, A. / Jerala, R.
History
DepositionOct 27, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2020Group: Database references / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_assembly ...pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref / struct_ref_seq
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lactoferrin-based synthetic peptide FQWQRNIRKVR


Theoretical massNumber of molelcules
Total (without water)1,5331
Polymers1,5331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint1 kcal/mol
Surface area1950 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)7 / 20target function
RepresentativeModel #4closest to the average

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Components

#1: Protein/peptide lactoferrin-based synthetic peptide FQWQRNIRKVR


Mass: 1532.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 2mM Lf11; 20mM sodium phosphate buffer (pH 5.5), 92% H20, 8% D20
Solvent system: 92% H20, 8% D20
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert,P., Braun,W., Wuthrich,Kstructure solution
DYANA1.5Guntert,P., Braun,W., Wuthrich,Krefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 7

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