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- PDB-1cou: ANTICOAGULANT PROTEIN FROM THE NEMATODE ANCYLOSTOMA CANINUM -

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Basic information

Entry
Database: PDB / ID: 1cou
TitleANTICOAGULANT PROTEIN FROM THE NEMATODE ANCYLOSTOMA CANINUM
ComponentsPROTEIN (NEMATODE ANTICOAGULANT PROTEIN C2)
KeywordsBLOOD CLOTTING / ANTICOAGULANT / PROTEASE INHIBITOR
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / Laminin / Laminin / Ribbon / Mainly Beta
Similarity search - Domain/homology
Anti-coagulant protein C2
Similarity search - Component
Biological speciesAncylostoma caninum (dog hookworm)
MethodSOLUTION NMR / molecular dynamics
AuthorsDuggan, B.M. / Dyson, H.J. / Wright, P.E.
Citation
Journal: Eur.J.Biochem. / Year: 1999
Title: Inherent flexibility in a potent inhibitor of blood coagulation, recombinant nematode anticoagulant protein c2.
Authors: Duggan, B.M. / Dyson, H.J. / Wright, P.E.
History
DepositionMay 28, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (NEMATODE ANTICOAGULANT PROTEIN C2)


Theoretical massNumber of molelcules
Total (without water)9,7581
Polymers9,7581
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)18 / 100LEAST RESTRAINT VIOLATIONS AND LOWEST ENERGIES
RepresentativeModel #14

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Components

#1: Protein PROTEIN (NEMATODE ANTICOAGULANT PROTEIN C2) / NAPC2


Mass: 9757.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylostoma caninum (dog hookworm) / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q16938

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQ-COSY
13115N HSQC
14115N NOESY-HSQC
15115N TOCSY-HSQC
16115N HSQC-NOESY-HSQC
171HNHA
18113C HSQC
19115N {1H} NOE

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Sample preparation

DetailsContents: 0.050 M NACL, 0.000020 M DSS AND EITHER 95% H2O/5% D2O OR 99.99% D2O
Sample conditionsIonic strength: 0.05 M / pH: 4.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker AMX600BrukerAMX6006002
Bruker DMX750BrukerDMX7507503

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Processing

NMR software
NameVersionDeveloperClassification
Amber5.1CASE, PEARLMAN, CALDWELL, CHEATHAM, ROSS, SIMMERLING, DARDEN, MERZ, SEIBEL, STANTON, CHENG, VINCENT, CROWLEY, FERGUSON, RADMER, SINGH, WEINER, KOLLMANrefinement
Felix95structure solution
Felix97structure solution
DYANAstructure solution
Amber5.1structure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS AND LOWEST ENERGIES
Conformers calculated total number: 100 / Conformers submitted total number: 18

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