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- PDB-1zaq: FOURTH EGF-LIKE DOMAIN OF THROMBOMODULIN, NMR, 12 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1zaq
TitleFOURTH EGF-LIKE DOMAIN OF THROMBOMODULIN, NMR, 12 STRUCTURES
ComponentsTHROMBOMODULIN
KeywordsBLOOD COAGULATION / ANTICOAGULANT / FIBRINOGEN / PEPTIDE SYNTHESIS / PROTEIN C / THROMBIN
Function / homology
Function and homology information


blood coagulation, common pathway / negative regulation of blood coagulation / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / negative regulation of platelet activation / response to X-ray / negative regulation of fibrinolysis / Common Pathway of Fibrin Clot Formation ...blood coagulation, common pathway / negative regulation of blood coagulation / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / negative regulation of platelet activation / response to X-ray / negative regulation of fibrinolysis / Common Pathway of Fibrin Clot Formation / response to cAMP / female pregnancy / Cell surface interactions at the vascular wall / transmembrane signaling receptor activity / blood coagulation / signaling receptor activity / response to lipopolysaccharide / external side of plasma membrane / calcium ion binding / cell surface / proteolysis / extracellular space / plasma membrane
Similarity search - Function
Thrombomodulin-like, EGF-like / Thrombomodulin like fifth domain, EGF-like / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Calcium-binding EGF domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / Coagulation Factor Xa inhibitory site ...Thrombomodulin-like, EGF-like / Thrombomodulin like fifth domain, EGF-like / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Calcium-binding EGF domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / Coagulation Factor Xa inhibitory site / Laminin / Laminin / C-type lectin-like/link domain superfamily / EGF-type aspartate/asparagine hydroxylation site / C-type lectin fold / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsMeininger, D.P. / Komives, E.A.
CitationJournal: Protein Sci. / Year: 1995
Title: Synthesis, Activity, and Preliminary Structure of the Fourth Egf-Like Domain of Thrombomodulin
Authors: Meininger, D.P. / Hunter, M.J. / Komives, E.A.
History
DepositionSep 9, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THROMBOMODULIN


Theoretical massNumber of molelcules
Total (without water)5,0781
Polymers5,0781
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / -
Representative

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Components

#1: Protein/peptide THROMBOMODULIN / / TM4


Mass: 5077.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD VESSEL / Cellular location: CELL SURFACECell membrane / Organ: PRIMARILY LUNG / References: UniProt: P07204

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
DGIIHAVELrefinement
X-PLORBRUNGERrefinement
NMR ensembleConformers submitted total number: 12

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