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- PDB-9tls: De novo designed single-chain antiparallel coiled-coil hairpin wi... -

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Basic information

Entry
Database: PDB / ID: 9tls
TitleDe novo designed single-chain antiparallel coiled-coil hairpin with binding site for KLHL20, Sc-apCC-2-KLHL20-3
ComponentsSc-apCC-2-KLHL20-3
KeywordsDE NOVO PROTEIN / Protein Binder / Computational Design / Coiled-coil
Function / homologyISOPROPYL ALCOHOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMylemans, B. / Woolfson, D.N.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006231/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006703/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V008412/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V008412/2 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: De Novo-Designed Bifunctional
Authors: Mylemans, B. / Korona, B. / Acevedo-Jake, A.M. / MacRae, A. / Edwards, T.A. / Huang, D.T. / Wilson, A.J. / Itzhaki, L.S. / Woolfson, D.N.
History
DepositionDec 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sc-apCC-2-KLHL20-3
B: Sc-apCC-2-KLHL20-3
C: Sc-apCC-2-KLHL20-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7058
Polymers25,3403
Non-polymers3645
Water5,350297
1
A: Sc-apCC-2-KLHL20-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6594
Polymers8,4471
Non-polymers2123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sc-apCC-2-KLHL20-3


Theoretical massNumber of molelcules
Total (without water)8,4471
Polymers8,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sc-apCC-2-KLHL20-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5993
Polymers8,4471
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.903, 31.910, 75.183
Angle α, β, γ (deg.)90.000, 93.523, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Sc-apCC-2-KLHL20-3


Mass: 8446.743 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES 10% PEG 5000 MME 12 % 1-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.62 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 1.45→29.37 Å / Num. obs: 42389 / % possible obs: 99.88 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.34 Å2 / CC1/2: 1 / Net I/σ(I): 12.22
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 4145 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→29.37 Å / SU ML: 0.1673 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2104 2124 5.01 %
Rwork0.1804 40255 -
obs0.182 42379 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.85 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 24 297 2043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551812
X-RAY DIFFRACTIONf_angle_d0.77852451
X-RAY DIFFRACTIONf_chiral_restr0.0532287
X-RAY DIFFRACTIONf_plane_restr0.0093328
X-RAY DIFFRACTIONf_dihedral_angle_d13.715709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.29751350.25252609X-RAY DIFFRACTION98.53
1.48-1.520.27241460.22392700X-RAY DIFFRACTION99.89
1.52-1.560.26281500.21262621X-RAY DIFFRACTION99.96
1.56-1.610.25281150.19922702X-RAY DIFFRACTION100
1.61-1.660.2221150.19382664X-RAY DIFFRACTION99.96
1.66-1.720.22861300.20962667X-RAY DIFFRACTION100
1.72-1.790.23751400.20392705X-RAY DIFFRACTION100
1.79-1.870.2491340.20012676X-RAY DIFFRACTION100
1.87-1.970.23171490.1962642X-RAY DIFFRACTION100
1.97-2.090.27141700.18852666X-RAY DIFFRACTION100
2.09-2.250.19341310.16792698X-RAY DIFFRACTION100
2.25-2.480.18691400.16742692X-RAY DIFFRACTION100
2.48-2.840.21961410.17982704X-RAY DIFFRACTION100
2.84-3.570.20321380.17142746X-RAY DIFFRACTION100
3.57-29.370.18241900.16732763X-RAY DIFFRACTION99.93

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