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- PDB-2lkq: NMR structure of the lambda 5 22-45 peptide -

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Basic information

Entry
Database: PDB / ID: 2lkq
TitleNMR structure of the lambda 5 22-45 peptide
ComponentsImmunoglobulin lambda-like polypeptide 1
KeywordsIMMUNE SYSTEM / pre-BCR / b cell development
Function / homology
Function and homology information


IgG immunoglobulin complex / immunoglobulin mediated immune response / Cell surface interactions at the vascular wall / antigen binding / immune response / endoplasmic reticulum / extracellular region / membrane
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin lambda-like polypeptide 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsElantak, L. / Espeli, M. / Boned, A. / Bornet, O. / Breton, C. / Feracci, M. / Roche, P. / Guerlesquin, F. / Schiff, C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Basis for Galectin-1-dependent Pre-B Cell Receptor (Pre-BCR) Activation.
Authors: Elantak, L. / Espeli, M. / Boned, A. / Bornet, O. / Bonzi, J. / Gauthier, L. / Feracci, M. / Roche, P. / Guerlesquin, F. / Schiff, C.
History
DepositionOct 19, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin lambda-like polypeptide 1


Theoretical massNumber of molelcules
Total (without water)2,8561
Polymers2,8561
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Immunoglobulin lambda-like polypeptide 1 / CD179 antigen-like family member B / Ig lambda-5 / Immunoglobulin omega polypeptide / ...CD179 antigen-like family member B / Ig lambda-5 / Immunoglobulin omega polypeptide / Immunoglobulin-related protein 14.1


Mass: 2856.279 Da / Num. of mol.: 1 / Fragment: UNP residues 59-82 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15814

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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

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Sample preparation

DetailsContents: 20 mM potassium phosphate, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 20 mM / Component: potassium phosphate-1
Sample conditionsIonic strength: 0 / pH: 5.2 / Pressure: ambient / Temperature: 303 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
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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