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- PDB-1y1b: Solution structure of Anemonia elastase inhibitor -

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Basic information

Entry
Database: PDB / ID: 1y1b
TitleSolution structure of Anemonia elastase inhibitor
ComponentsElastase inhibitor
KeywordsHYDROLASE INHIBITOR / non-classical / Kazal-type / protease inhibitor / CSH motif
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / : / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MethodSOLUTION NMR / simulated annealing
AuthorsHemmi, H. / Kumazaki, T. / Yoshizawa-Kumagaye, K. / Nishiuchi, Y. / Yoshida, T. / Ohkubo, T. / Kobayashi, Y.
CitationJournal: Biochemistry / Year: 2005
Title: Structural and Functional Study of an Anemonia Elastase Inhibitor, a "Nonclassical" Kazal-Type Inhibitor from Anemonia sulcata
Authors: Hemmi, H. / Kumazaki, T. / Yoshizawa-Kumagaye, K. / Nishiuchi, Y. / Yoshida, T. / Ohkubo, T. / Kobayashi, Y.
History
DepositionNov 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elastase inhibitor


Theoretical massNumber of molelcules
Total (without water)5,1391
Polymers5,1391
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 / 200structures with the lowest energy
RepresentativeModel #14lowest energy

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Components

#1: Protein/peptide Elastase inhibitor


Mass: 5138.986 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is modified from the sequence occuring naturally in sea anemone Anemonia sulcata ((Snake-locks sea anemone).
References: UniProt: P16895
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
1412D ROESY
151E-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 3mM Anemonia elastase inhibitor; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: NA / pH: 2.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker DRXBrukerDRX6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukerprocessing
Sparky3Goddard, Knellerdata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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