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- PDB-36iq: Structure of de novo designed doxorubicin binding protein with do... -

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Basic information

Entry
Database: PDB / ID: 36iq
TitleStructure of de novo designed doxorubicin binding protein with doxorubicin bound
ComponentsDe novo designed doxorubicin-binding protein
KeywordsDE NOVO PROTEIN / De novo design
Function / homologyDOXORUBICIN
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsHorst, M. / Ouchida, S. / DeGrado, W.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122603 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM163375 United States
CitationJournal: To Be Published
Title: Pi-pi sandwich guided design of a de novo doxorubicin-binding protein
Authors: Ouchida, S. / Gou, X. / Horst, M. / Bakanas, I. / Ashworth, A. / DeGrado, W.F.
History
DepositionJun 11, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed doxorubicin-binding protein
B: De novo designed doxorubicin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3864
Polymers22,2992
Non-polymers1,0872
Water1,11762
1
A: De novo designed doxorubicin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6932
Polymers11,1491
Non-polymers5441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: De novo designed doxorubicin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6932
Polymers11,1491
Non-polymers5441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.700, 42.700, 174.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

21A-243-

HOH

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Components

#1: Protein De novo designed doxorubicin-binding protein


Mass: 11149.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN


Mass: 543.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H29NO11 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.93 Å3/Da / Density % sol: 54.6 % / Description: Hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 500 mM HEPES, 489 mM Sodium Citrate,68.5 mM Sodium Chloride, 5 mM Sodium phosphate dibasic, 0.9 mM Potassium phosphate monobasic, 1.35 mM Potassium chloride, pH 7.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11582 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2026
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11582 Å / Relative weight: 1
ReflectionResolution: 1.56→87.35 Å / Num. obs: 27441 / % possible obs: 99.7 % / Redundancy: 35.3 % / Biso Wilson estimate: 25.66 Å2 / Rmerge(I) obs: 0.177 / Rrim(I) all: 0.182 / Χ2: 0.99 / Net I/σ(I): 19
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 30.6 % / Rmerge(I) obs: 1.557 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1348 / Rrim(I) all: 1.609 / Χ2: 0.67

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Processing

Software
NameVersionClassification
PHENIX2.0_5848refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
Servalcatrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→58.24 Å / SU ML: 0.2069 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.8922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 1999 7.31 %
Rwork0.2184 25364 -
obs0.2211 27363 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.81 Å2
Refinement stepCycle: LAST / Resolution: 1.56→58.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1421 0 78 62 1561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00991551
X-RAY DIFFRACTIONf_angle_d0.99352114
X-RAY DIFFRACTIONf_chiral_restr0.0531230
X-RAY DIFFRACTIONf_plane_restr0.0087267
X-RAY DIFFRACTIONf_dihedral_angle_d25.6801578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.31541410.29171764X-RAY DIFFRACTION99.69
1.6-1.640.32231380.27711809X-RAY DIFFRACTION99.69
1.64-1.690.29791390.28361766X-RAY DIFFRACTION99.58
1.69-1.750.34421370.29281732X-RAY DIFFRACTION99.15
1.75-1.810.33681400.31551791X-RAY DIFFRACTION99.38
1.81-1.880.38351410.33321778X-RAY DIFFRACTION99.48
1.88-1.960.3151370.24481776X-RAY DIFFRACTION99.69
1.97-2.070.24071440.21221798X-RAY DIFFRACTION100
2.07-2.20.22761390.19471808X-RAY DIFFRACTION99.95
2.2-2.370.21691440.19191829X-RAY DIFFRACTION99.8
2.37-2.610.23361440.20071799X-RAY DIFFRACTION99.95
2.61-2.980.22961440.21721846X-RAY DIFFRACTION100
2.98-3.760.23281500.20341875X-RAY DIFFRACTION100
3.76-58.240.26181610.20911993X-RAY DIFFRACTION99.81

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