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- PDB-2mcr: Solution structure of ShK-like immunomodulatory peptide from Brug... -

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Basic information

Entry
Database: PDB / ID: 2mcr
TitleSolution structure of ShK-like immunomodulatory peptide from Brugia malayi (filarial worm)
ComponentsProbable zinc metalloproteinase, putative
KeywordsIMMUNE SYSTEM / worms / BmK1 / ShK-like peptide / Kv1.3
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
ShK toxin domain / ShK domain-like / Astacin-like metallopeptidase domain / ShKT domain / ShKT domain profile. / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
Metalloendopeptidase / :
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsChhabra, S. / Swarbrick, J.D. / Pennington, M.W. / Chang, S.C. / Norton, R.S.
CitationJournal: Faseb J. / Year: 2014
Title: Kv1.3 channel-blocking immunomodulatory peptides from parasitic worms: implications for autoimmune diseases.
Authors: Chhabra, S. / Chang, S.C. / Nguyen, H.M. / Huq, R. / Tanner, M.R. / Londono, L.M. / Estrada, R. / Dhawan, V. / Chauhan, S. / Upadhyay, S.K. / Gindin, M. / Hotez, P.J. / Valenzuela, J.G. / ...Authors: Chhabra, S. / Chang, S.C. / Nguyen, H.M. / Huq, R. / Tanner, M.R. / Londono, L.M. / Estrada, R. / Dhawan, V. / Chauhan, S. / Upadhyay, S.K. / Gindin, M. / Hotez, P.J. / Valenzuela, J.G. / Mohanty, B. / Swarbrick, J.D. / Wulff, H. / Iadonato, S.P. / Gutman, G.A. / Beeton, C. / Pennington, M.W. / Norton, R.S. / Chandy, K.G.
History
DepositionAug 22, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Apr 27, 2016Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable zinc metalloproteinase, putative


Theoretical massNumber of molelcules
Total (without water)4,1831
Polymers4,1831
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)30 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Probable zinc metalloproteinase, putative


Mass: 4182.894 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Brugia malayi (agent of lymphatic filariasis)
References: UniProt: A8PQK5, UniProt: A0A0J9XQE3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D 1H-15N HSQC
2212D 1H-13C HSQC
2322D 1H-1H NOESY
1422D 1H-1H NOESY
2522D 1H-1H TOCSY
2612D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM entity, 10 mM sodium phosphate, 100 % D2O, 100% D2O100% D2O
20.8 mM entity, 10 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.8 mMentity-11
10 mMsodium phosphate-21
100 %D2O-31
0.8 mMentity-42
10 mMsodium phosphate-52
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.8ambient 293 K
24.8ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmrCCPNchemical shift assignment
TopSpin3.2Bruker Biospincollection
XPLOR_NIHBRUNGERrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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