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- PDB-9gw6: Lys9DabMC6*a 2-Delta -

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Basic information

Entry
Database: PDB / ID: 9gw6
TitleLys9DabMC6*a 2-Delta
Components
  • ACE-ASP-GLU-AIB-GLN-LEU-SER-AIB-GLN-DAB-ARG-NH2
  • ACE-ASP-LEU-GLN-GLN-LEU-HIS-SER-GLN-LYS-ARG-LYS-ILE-THR-LEU-NH2
KeywordsDE NOVO PROTEIN / ALPHA-HELIX / DESIGN / MINIATURIZED METALLOPROTEINS
Function / homologyCO(III)-(DEUTEROPORPHYRIN IX) / HYDROXIDE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsMaglio, O. / Lombardi, A. / Chino, M. / Pirro, F.
Funding support1items
OrganizationGrant numberCountry
Other government
Citation
Journal: Inorg.Chem. / Year: 2026
Title: Iron to cobalt swapping in a bioinspired heme-peroxidase: structural characterization and functional implications
Authors: Chino, M. / Cerrone, C. / Pirro, F. / De Fenza, M. / Demeshko, S. / Maglio, O. / Meyer, F. / Lombardi, A.
#1: Journal: Chem Comm / Year: 2021
Title: Histidine orientation in artificial peroxidase regioisomers as determined by paramagnetic NMR shifts
Authors: Maglio, O. / Chino, M. / Vicari, C. / Pavone, V. / Louro, R. / Lombardi, A.
#2: Journal: Chemistry / Year: 2003
Title: Design of a new mimochrome with unique topology
Authors: Lombardi, A. / Nastri, F. / Marasco, D. / De Sanctis, G. / Sinibaldi, F. / Santucci, R. / Coletta, M. / Pavone, V.
History
DepositionSep 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACE-ASP-GLU-AIB-GLN-LEU-SER-AIB-GLN-DAB-ARG-NH2
B: ACE-ASP-LEU-GLN-GLN-LEU-HIS-SER-GLN-LYS-ARG-LYS-ILE-THR-LEU-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4914
Polymers2,9062
Non-polymers5852
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ACE-ASP-GLU-AIB-GLN-LEU-SER-AIB-GLN-DAB-ARG-NH2


Mass: 1170.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Protein/peptide ACE-ASP-LEU-GLN-GLN-LEU-HIS-SER-GLN-LYS-ARG-LYS-ILE-THR-LEU-NH2


Mass: 1736.048 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical ChemComp-DEU / CO(III)-(DEUTEROPORPHYRIN IX)


Mass: 567.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28CoN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
Has ligand of interestY
Has protein modificationY

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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 TOCSY
121isotropic12D DQF-COSY
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 0.50 mM None MC6*a2-Delta, 50%H2O/40%TFE / Label: None / Solvent system: 50%H2O/40%TFE
SampleConc.: 0.50 mM / Component: MC6*a2-Delta / Isotopic labeling: None
Sample conditionsIonic strength: Trifluoroacetate Not defined / Label: 1 / pH: 4.6 pD / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: With cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Amber10Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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