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- PDB-1dn3: NMR STRUCTURE OF A MODEL HYDROPHILIC AMPHIPATHIC HELICAL BASIC PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1dn3
TitleNMR STRUCTURE OF A MODEL HYDROPHILIC AMPHIPATHIC HELICAL BASIC PEPTIDE
ComponentsHUMAN PLATELET FACTOR 4, SEGMENT 59-73
KeywordsDE NOVO PROTEIN / HYDROPHILIC AMPHIPATHIC BASIC HELIX MODEL
Function / homology
Function and homology information


CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / negative regulation of MHC class II biosynthetic process / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / killing by host of symbiont cells / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity ...CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / negative regulation of MHC class II biosynthetic process / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / killing by host of symbiont cells / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / defense response to protozoan / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of megakaryocyte differentiation / Common Pathway of Fibrin Clot Formation / negative regulation of angiogenesis / neutrophil chemotaxis / platelet alpha granule lumen / Cell surface interactions at the vascular wall / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation / cytokine-mediated signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of cell population proliferation / G alpha (i) signalling events / collagen-containing extracellular matrix / cellular response to lipopolysaccharide / inflammatory response / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytoplasm
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model type detailsminimized average
AuthorsMontserret, R. / McLeish, M.J. / Bockmann, A. / Geourjon, C. / Penin, F.
CitationJournal: Biochemistry / Year: 2000
Title: Involvement of electrostatic interactions in the mechanism of peptide folding induced by sodium dodecyl sulfate binding.
Authors: Montserret, R. / McLeish, M.J. / Bockmann, A. / Geourjon, C. / Penin, F.
History
DepositionDec 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Aug 29, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_nat ...entity / entity_src_nat / pdbx_entity_src_syn / struct
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity.src_method / _struct.pdbx_descriptor
Revision 1.5Apr 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN PLATELET FACTOR 4, SEGMENT 59-73


Theoretical massNumber of molelcules
Total (without water)1,6081
Polymers1,6081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide HUMAN PLATELET FACTOR 4, SEGMENT 59-73


Mass: 1607.890 Da / Num. of mol.: 1 / Mutation: L59A I63A, I64A, L68A / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) Homo sapiens (human) / References: UniProt: P02776

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF COSY
131TOCSY
1411H 13C HSQC
1511H 13C HSQC TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR AND 1H-13C HETERONUCLEAR METHODS

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Sample preparation

DetailsContents: 40 MM D25 SODIUM DODECYL SULFATE 98% 10 MM SODIUM PHOSPHATE BUFFER PH 6.0
Sample conditionspH: 6.0 / Pressure: AMBIENT / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1VARIAN INC.collection
X-PLOR3.1BRUNGER, A.T.structure solution
X-PLOR3.1BRUNGER, A.T.refinement
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 1

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