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- PDB-9mxg: GRN-P4A mutant, granulin -

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Basic information

Entry
Database: PDB / ID: 9mxg
TitleGRN-P4A mutant, granulin
ComponentsGranulin peptide
KeywordsCYTOKINE / PROTEIN
Function / homologyGranulins signature. / Granulin family / Granulin / Granulin superfamily / Granulin / Granulin / extracellular region / Granulin
Function and homology information
Biological speciesOpisthorchis viverrini (Southeast Asian liver fluke)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRaffaelli, T. / Daly, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Topological isomers of a potent wound healing peptide: structural insights and implications for bioactivity.
Authors: Raffaelli, T. / Wilson, D.T. / Mobli, M. / Smout, M.J. / Zhao, G. / Takjoo, R. / Bansal, P.S. / Yu, R. / Zhang, Z. / Loukas, A. / Daly, N.L.
History
DepositionJan 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Granulin peptide


Theoretical massNumber of molelcules
Total (without water)2,5271
Polymers2,5271
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Granulin peptide


Mass: 2526.918 Da / Num. of mol.: 1 / Fragment: residues 30-53 / Mutation: P2G, P4A / Source method: obtained synthetically
Source: (synth.) Opisthorchis viverrini (Southeast Asian liver fluke)
References: UniProt: B8XSI4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D COSY
121anisotropic12D TOCSY
131anisotropic12D NOESY
141anisotropic12D 1H-13C HSQC
151anisotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 0.2 mM peptide, 90% H2O/10% D2O / Label: GRN-L1m / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.2 mM / Component: peptide / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 M / Label: 90% H2O/10% D2O / pH: 5 / Pressure: AMBIENT / Temperature: 290 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
TopSpin3.98.15Bruker Biospincollection
CcpNmr Analysis3.98.15CCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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