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- PDB-5yhn: Solution structure of the LEKTI Domain 4 -

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Basic information

Entry
Database: PDB / ID: 5yhn
TitleSolution structure of the LEKTI Domain 4
ComponentscDNA FLJ60407, highly similar to Serine protease inhibitor Kazal-type 5
KeywordsHYDROLASE INHIBITOR / Kazal / inhibitor / LEKTI
Function / homology
Function and homology information


negative regulation of antibacterial peptide production / epidermal lamellar body / regulation of timing of anagen / epidermal cell differentiation / hair cell differentiation / Formation of the cornified envelope / negative regulation of immune response / regulation of T cell differentiation / regulation of cell adhesion / epithelial cell differentiation ...negative regulation of antibacterial peptide production / epidermal lamellar body / regulation of timing of anagen / epidermal cell differentiation / hair cell differentiation / Formation of the cornified envelope / negative regulation of immune response / regulation of T cell differentiation / regulation of cell adhesion / epithelial cell differentiation / extracellular matrix organization / negative regulation of angiogenesis / central nervous system development / negative regulation of proteolysis / serine-type endopeptidase inhibitor activity / cell cortex / cell differentiation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular region / cytosol / cytoplasm
Similarity search - Function
Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile.
Similarity search - Domain/homology
cDNA FLJ60407, highly similar to Serine protease inhibitor Kazal-type 5 / Serine protease inhibitor Kazal-type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMok, Y.K. / Ramesh, K.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore) Singapore
CitationJournal: Structure / Year: 2018
Title: Homologous Lympho-Epithelial Kazal-type Inhibitor Domains Delay Blood Coagulation by Inhibiting Factor X and XI with Differential Specificity.
Authors: Ramesh, K. / Lama, D. / Tan, K.W. / Nguyen, V.S. / Chew, F.T. / Verma, C.S. / Mok, Y.K.
History
DepositionSep 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cDNA FLJ60407, highly similar to Serine protease inhibitor Kazal-type 5


Theoretical massNumber of molelcules
Total (without water)8,0291
Polymers8,0291
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5460 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein cDNA FLJ60407, highly similar to Serine protease inhibitor Kazal-type 5 / LEKTI


Mass: 8029.053 Da / Num. of mol.: 1 / Fragment: Domain 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B4DWS3, UniProt: Q9NQ38*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D (H)CCH-TOCSY
131isotropic13D CBCA(CO)NH
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM 13C 15N LEKTI Domain 4, 90% H2O/10% D2O / Details: 10mM Sodium Acetate pH 4.6 / Label: LEKTI Domain 4 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: LEKTI Domain 4 / Isotopic labeling: 13C 15N
Sample conditionsIonic strength: 10 mM / Label: d4 / pH: 4.6 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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