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- PDB-6f27: NMR solution structure of non-bound [des-Arg10]-kallidin (DAKD) -

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Basic information

Entry
Database: PDB / ID: 6f27
TitleNMR solution structure of non-bound [des-Arg10]-kallidin (DAKD)
ComponentsDAKD
KeywordsMEMBRANE PROTEIN / GPCR G-protein-coupled receptor peptide bradykinin kallidin human kinin
Function / homology
Function and homology information


negative regulation of blood coagulation / negative regulation of cell adhesion / cysteine-type endopeptidase inhibitor activity / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / Post-translational protein phosphorylation / negative regulation of proteolysis / hormone activity / vasodilation ...negative regulation of blood coagulation / negative regulation of cell adhesion / cysteine-type endopeptidase inhibitor activity / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / Post-translational protein phosphorylation / negative regulation of proteolysis / hormone activity / vasodilation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / heparin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / inflammatory response / positive regulation of apoptotic process / endoplasmic reticulum lumen / signaling receptor binding / extracellular space / extracellular exosome / zinc ion binding / extracellular region / plasma membrane
Similarity search - Function
HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing
AuthorsRichter, C. / Jonker, H.R.A. / Schwalbe, H. / Joedicke, L. / Mao, J. / Kuenze, G. / Reinhart, C. / Kalavacherla, T. / Meiler, J. / Preu, J. ...Richter, C. / Jonker, H.R.A. / Schwalbe, H. / Joedicke, L. / Mao, J. / Kuenze, G. / Reinhart, C. / Kalavacherla, T. / Meiler, J. / Preu, J. / Michel, H. / Glaubitz, C.
Funding support Germany, United States, 3items
OrganizationGrant numberCountry
German Research FoundationG-NMR, SFB 807, GL 307/8-1, Macromolecular Complexes Germany
State of HesseBMRZ Germany
NIH and NSFR01 GM080403, R01 GM099842, R01 GM073151, CHE 1305874 United States
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: The molecular basis of subtype selectivity of human kinin G-protein-coupled receptors.
Authors: Joedicke, L. / Mao, J. / Kuenze, G. / Reinhart, C. / Kalavacherla, T. / Jonker, H.R.A. / Richter, C. / Schwalbe, H. / Meiler, J. / Preu, J. / Michel, H. / Glaubitz, C.
History
DepositionNov 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.6Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DAKD


Theoretical massNumber of molelcules
Total (without water)1,0341
Polymers1,0341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1210 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide DAKD / Alpha-2-thiol proteinase inhibitor / Fitzgerald factor / High molecular weight kininogen / HMWK / ...Alpha-2-thiol proteinase inhibitor / Fitzgerald factor / High molecular weight kininogen / HMWK / Williams-Fitzgerald-Flaujeac factor / [des-Arg10]-kallidin [Lys-des-Arg9]-Bradykinin


Mass: 1034.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01042

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H ROESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC (edited)
141isotropic12D 1H-13C HMBC
151isotropic12D 1H-15N HMQC (SOFAST)

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Sample preparation

DetailsType: solution
Contents: 3 mM DAKD, 50 mM MES, 100 mM sodium chloride, 90% H2O/10% D2O
Label: sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMDAKDnatural abundance1
50 mMMESnatural abundance1
100 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 111 mM / Label: normal / pH: 5.6 / Pressure: ambient mbar / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz / Details: prodigy cryogenic triple-resonance probe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
TopSpin3.5Bruker Biospinprocessing
Sparky3.114Goddard and Knellerchemical shift assignment
Sparky3.114Goddard and Knellerpeak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA1.2 HJ webportal versionLinge, O'Donoghue and Nilgesrefinement
TALOSNShen and Baxdata analysis
Refinement
MethodSoftware ordinalDetails
torsion angle dynamics5structure determination
simulated annealing6refinement in water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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