[English] 日本語
Yorodumi
- PDB-1h0z: LEKTI domain six -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h0z
TitleLEKTI domain six
ComponentsSERINE PROTEASE INHIBITOR KAZAL-TYPE 5, CONTAINS HEMOFILTRATE PEPTIDE HF6478, HEMOFILTRATE PEPTIDE HF7665
KeywordsSERINE PROTEINASE INHIBITOR
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 / negative regulation of angiogenesis / extracellular matrix organization / 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 / cytoplasm / cytosol
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 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLauber, T. / Roesch, P. / Marx, U.C.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Homologous Proteins with Different Folds: The Three-Dimensional Structures of Domains 1 and 6 of the Multiple Kazal-Type Inhibitor Lekti
Authors: Lauber, T. / Schulz, A. / Schweimer, K. / Adermann, K. / Marx, U.C.
History
DepositionJul 1, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_sheet
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_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE PROTEASE INHIBITOR KAZAL-TYPE 5, CONTAINS HEMOFILTRATE PEPTIDE HF6478, HEMOFILTRATE PEPTIDE HF7665


Theoretical massNumber of molelcules
Total (without water)7,6831
Polymers7,6831
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)21 / 60LEAST ENERGY AND LEAST RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein SERINE PROTEASE INHIBITOR KAZAL-TYPE 5, CONTAINS HEMOFILTRATE PEPTIDE HF6478, HEMOFILTRATE PEPTIDE HF7665 / HF7665 / LYMPHO-EPITHELIAL KAZAL-TYPE RELATED INHIBITOR / LEKTI


Mass: 7682.533 Da / Num. of mol.: 1 / Fragment: LEKTI DOMAIN SIX (HF7665), RESIDUES 356-423 / Source method: isolated from a natural source
Details: DISULFIDE LINKAGE BETWEEN CYS A12 AND CYS A48, AND BETWEEN CYS A26 AND CYS A45
Source: (natural) HOMO SAPIENS (human) / Cell: LYMPHO EPITHELIAL CELLS / Organ: BLOOD / References: UniProt: Q9NQ38
Sequence detailsTHE SEQUENCE OF THE PROTEIN USED IN THE NMR STUDY DIFFERS FROM THAT OF THE MATCHING SWISS-PROT ...THE SEQUENCE OF THE PROTEIN USED IN THE NMR STUDY DIFFERS FROM THAT OF THE MATCHING SWISS-PROT ENTRY AT POSITION 420. RESIDUE 420 IS A GLU, NOT LYS AS IN THE SWISS-PROT ENTRY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131CLEAN-TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING STANDARD 2D NMR EXPERIMENTS ON A NATIVE PROTEIN SAMPLE ISOLATED FROM HUMAN BLOOD FILTRATE

-
Sample preparation

Sample conditionspH: 4.0 / Temperature: 298 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST ENERGY AND LEAST RESTRAINT VIOLATION
Conformers calculated total number: 60 / Conformers submitted total number: 21

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more