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- PDB-9ppu: Beta-sandwich forming metallopeptide -

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Basic information

Entry
Database: PDB / ID: 9ppu
TitleBeta-sandwich forming metallopeptide
Components(De novo designed ...) x 2
KeywordsDE NOVO PROTEIN / Beta-sandwich / Copper / metallopeptide
Function / homology6-AMINOHEXANOIC ACID / COPPER (II) ION / FORMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å
AuthorsDang, V.T. / Nguyen, A.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM154793-01 United States
CitationJournal: Dalton Trans / Year: 2026
Title: A bis-macrocylic peptide ligand mimicking the beta-sandwich active site of multicopper oxidases.
Authors: Dang, V.T. / Drena, A. / Telser, J. / Wofford, L. / Nguyen, A.I.
History
DepositionJul 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: De novo designed metallopeptide
A: De novo designed metallopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5499
Polymers3,1072
Non-polymers4427
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, DOSY results show diffusion constant of 1.21 which corresponds to a mass 6x larger than the monomer. Mass and diffusion was compared to publish internal standard.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-22 kcal/mol
Surface area2310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.320, 41.320, 53.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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De novo designed ... , 2 types, 2 molecules BA

#1: Protein/peptide De novo designed metallopeptide


Mass: 1589.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide De novo designed metallopeptide


Mass: 1516.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 48 molecules

#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 6.0 M ammonium nitrate, 0.1 M BIS TRIS propane pH 7.0
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.36246 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36246 Å / Relative weight: 1
ReflectionResolution: 1.49→32.7 Å / Num. obs: 148327 / % possible obs: 97.98 % / Redundancy: 18.9 % / Biso Wilson estimate: 14.5 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1256 / Rpim(I) all: 0.0272 / Rrim(I) all: 0.1286 / Net I/σ(I): 19.31
Reflection shellResolution: 1.49→1.543 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.3702 / Mean I/σ(I) obs: 3.06 / Num. unique obs: 3336 / CC1/2: 0.905 / CC star: 0.975 / Rpim(I) all: 0.1664 / Rrim(I) all: 0.4084 / % possible all: 80.41

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: SAD / Resolution: 1.49→32.7 Å / SU ML: 0.1428 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.9324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1909 1425 10.13 %
Rwork0.1555 12636 -
obs0.1591 14061 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.63 Å2
Refinement stepCycle: LAST / Resolution: 1.49→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms219 0 22 41 282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089249
X-RAY DIFFRACTIONf_angle_d1.3462317
X-RAY DIFFRACTIONf_chiral_restr0.096628
X-RAY DIFFRACTIONf_plane_restr0.004934
X-RAY DIFFRACTIONf_dihedral_angle_d13.416380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.540.2131100.2091994X-RAY DIFFRACTION76.51
1.54-1.610.19891430.15091262X-RAY DIFFRACTION96.83
1.61-1.680.14561440.14341283X-RAY DIFFRACTION99.93
1.68-1.770.17491430.14761323X-RAY DIFFRACTION100
1.77-1.880.16751490.14521306X-RAY DIFFRACTION100
1.88-2.020.18241480.12621279X-RAY DIFFRACTION100
2.02-2.230.16341460.14641299X-RAY DIFFRACTION100
2.23-2.550.21361450.17771307X-RAY DIFFRACTION99.79
2.55-3.210.18561510.16491295X-RAY DIFFRACTION99.86
3.21-32.70.20931460.15361288X-RAY DIFFRACTION99.31

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