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- PDB-1fgd: EPIDERMAL GROWTH FACTOR (EGF) SUBDOMAIN OF HUMAN THROMBOMODULIN (... -

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Basic information

Entry
Database: PDB / ID: 1fgd
TitleEPIDERMAL GROWTH FACTOR (EGF) SUBDOMAIN OF HUMAN THROMBOMODULIN (NMR, 11 STRUCTURES)
ComponentsTHROMBOMODULIN
KeywordsBLOOD COAGULATION INHIBITOR / THROMBOMODULIN / EGF
Function / homology
Function and homology information


blood coagulation, common pathway / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / negative regulation of platelet activation / negative regulation of blood coagulation / response to X-ray / negative regulation of fibrinolysis / Common Pathway of Fibrin Clot Formation ...blood coagulation, common pathway / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / negative regulation of platelet activation / negative regulation of blood coagulation / 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 / blood coagulation / transmembrane signaling receptor activity / 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 ...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) / C-type lectin-like/link domain superfamily / Coagulation Factor Xa inhibitory site / C-type lectin fold / EGF-type aspartate/asparagine hydroxylation site / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsHrabal, R. / Komives, E.A. / Ni, F.
CitationJournal: Protein Sci. / Year: 1996
Title: Structural resiliency of an EGF-like subdomain bound to its target protein, thrombin.
Authors: Hrabal, R. / Komives, E.A. / Ni, F.
History
DepositionNov 28, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Revision 1.4Nov 6, 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: THROMBOMODULIN


Theoretical massNumber of molelcules
Total (without water)2,0181
Polymers2,0181
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)11 / -
Representative

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Components

#1: Protein/peptide THROMBOMODULIN


Mass: 2018.180 Da / Num. of mol.: 1
Fragment: C-TERMINAL SUBDOMAIN, RESIDUES 409 - 426, OF 5TH EPIDERMAL GROWTH FACTOR (EGF)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P07204
Has protein modificationY

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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

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 11

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