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- PDB-1dqb: NMR STRUCTURE OF THROMBOMODULIN EGF(4-5) -

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Basic information

Entry
Database: PDB / ID: 1dqb
TitleNMR STRUCTURE OF THROMBOMODULIN EGF(4-5)
ComponentsTHROMBOMODULIN
KeywordsMEMBRANE PROTEIN / THROMBIN / EGF MODULE / ANTICOAGULANT / GLYCOSYLATION
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 / distance geometry simulated annealing refinment
AuthorsWood, M.J. / Sampoli-Benitez, B.A. / Komives, E.A.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Solution structure of the smallest cofactor-active fragment of thrombomodulin.
Authors: Wood, M.J. / Sampoli-Benitez, B.A. / Komives, E.A.
History
DepositionJan 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nmr_software / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THROMBOMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7433
Polymers9,3001
Non-polymers4422
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 / 50structures with the least restraint violations
RepresentativeModel #9lowest energy

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Components

#1: Protein THROMBOMODULIN /


Mass: 9300.352 Da / Num. of mol.: 1 / Fragment: THE FOURTH AND FIFTH EGF-LIKE DOMAINS
Source method: isolated from a genetically manipulated source
Details: residues 346-426 / Source: (gene. exp.) Homo sapiens (human) / Cell: ENDOTHELIAL / Production host: Pichia pastoris (fungus) / References: UniProt: P07204
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1322D NOESY
NMR detailsText: This structure was calculated using NOEs from the 3D NOESY-HSQC and D2O NOESY and dihedral angles from the HNHA.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM TM45 U-15N; 90% H2O, 10% D2O, pH 6.590% H2O/10% D2O
21mM TM45; 100% D2O100% D2O
Sample conditionsIonic strength: 0 / pH: 6.5 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
Felix97Molecular Simulations Inc.data analysis
DGII97Molecular Simulations Inc.structure solution
X-PLOR3.5Brungerrefinement
RefinementMethod: distance geometry simulated annealing refinment / Software ordinal: 1
Details: The structures are based on 985 NOE distance restraints and 43 dihedral angle restraints and 16 streospecific assignments.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 12

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