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- PDB-2l1q: Solution structure of human Liver Expressed Antimicrobial Peptide 2 -

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Basic information

Entry
Database: PDB / ID: 2l1q
TitleSolution structure of human Liver Expressed Antimicrobial Peptide 2
ComponentsLiver-expressed antimicrobial peptide 2
KeywordsANTIMICROBIAL PROTEIN / polypeptide / disulfides / LEAP-2
Function / homology
Function and homology information


Antimicrobial peptides / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to bacterium / extracellular region
Similarity search - Function
Omega-AgatoxinV - #50 / Liver-expressed antimicrobial peptide 2 / Liver-expressed antimicrobial peptide 2 precursor (LEAP-2) / Omega-AgatoxinV / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Liver-expressed antimicrobial peptide 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsClark, R.J.
CitationJournal: Chembiochem / Year: 2010
Title: Structural and functional analysis of human liver-expressed antimicrobial peptide 2.
Authors: Henriques, S.T. / Tan, C.C. / Craik, D.J. / Clark, R.J.
History
DepositionAug 3, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 1, 2020Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Liver-expressed antimicrobial peptide 2


Theoretical massNumber of molelcules
Total (without water)4,5931
Polymers4,5931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Liver-expressed antimicrobial peptide 2


Mass: 4593.370 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LEAP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q969E1
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY

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Sample preparation

DetailsContents: 1 mM leap2-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: leap2-1
Sample conditionsIonic strength: 0 / pH: 3.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structures were calculated using torsion angle dynamics and subsequently refined by cartesian coordinate dynamics and powell minimization in explicit solvent using CNS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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