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- PDB-2n52: The solution structure of the kallikrein inhibitor SPINK6 -

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Basic information

Entry
Database: PDB / ID: 2n52
TitleThe solution structure of the kallikrein inhibitor SPINK6
ComponentsSerine protease inhibitor Kazal-type 6
KeywordsHYDROLASE INHIBITOR / inhibitor
Function / homology
Function and homology information


Formation of the cornified envelope / serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
: / Kazal serine protease inhibitors family signature. / 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
Serine protease inhibitor Kazal-type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsGrotzinger, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: The solution structure of the kallikrein-related peptidases inhibitor SPINK6.
Authors: Jung, S. / Fischer, J. / Spudy, B. / Kerkow, T. / Sonnichsen, F.D. / Xue, L. / Bonvin, A.M. / Goettig, P. / Magdolen, V. / Meyer-Hoffert, U. / Grotzinger, J.
History
DepositionJul 6, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / 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 / _struct_ref_seq_dif.details
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease inhibitor Kazal-type 6


Theoretical massNumber of molelcules
Total (without water)6,4111
Polymers6,4111
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 #1lowest energy

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Components

#1: Protein Serine protease inhibitor Kazal-type 6 / Kallikrein inhibitor


Mass: 6411.245 Da / Num. of mol.: 1 / Fragment: Kazal-like domain residues 21-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPINK6, UNQ844/PRO1782 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6UWN8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HNCO
1413D H(CCO)NH
1513D HN(CO)CA
1613D HN(COCA)CB
1713D HN(CA)CB
1813D 1H-15N TOCSY
1913D 1H-13C NOESY
11013D 1H-15N NOESY
11113D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] protein, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 0.5 mM / Component: entity-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.15 / pH: 7.4 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR softwareName: CYANA / Developer: Guntert P. / Classification: refinement
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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