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- PDB-9tlm: De Novo designed single-chain antiparallel coiled-coil hairpin wi... -

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Basic information

Entry
Database: PDB / ID: 9tlm
TitleDe Novo designed single-chain antiparallel coiled-coil hairpin with binding site for MCL-1, Sc-apCC-2-MCL-1-1
ComponentsSc-apCC-2-MCL-1-1
KeywordsDE NOVO PROTEIN / Protein Binder / Computational Design / Coiled-coil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

Downloads & links

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Assembly

Deposited unit
A: Sc-apCC-2-MCL-1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6722
Polymers8,5801
Non-polymers921
Water97354
1
A: Sc-apCC-2-MCL-1-1
hetero molecules

A: Sc-apCC-2-MCL-1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3444
Polymers17,1602
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_654-x+y+1,y,-z-1/21
Buried area4320 Å2
ΔGint-34 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.578, 71.578, 90.456
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-230-

HOH

21A-236-

HOH

31A-254-

HOH

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Components

#1: Protein Sc-apCC-2-MCL-1-1


Mass: 8579.821 Da / Num. of mol.: 1
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.9 Å3/Da / Density % sol: 68.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Lithium sulphate, 0.1 M Sodium acetate 30% w/v PEG8000

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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 PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 1.8→30.99 Å / Num. obs: 13253 / % possible obs: 99.7 % / Redundancy: 39 % / Biso Wilson estimate: 35.73 Å2 / CC1/2: 1 / Net I/σ(I): 25.97
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 1274 / CC1/2: 0.789

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30.99 Å / SU ML: 0.2387 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.8501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.26 643 4.86 %
Rwork0.2458 12592 -
obs0.2465 13235 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 6 54 627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128591
X-RAY DIFFRACTIONf_angle_d1.0927796
X-RAY DIFFRACTIONf_chiral_restr0.060892
X-RAY DIFFRACTIONf_plane_restr0.0098107
X-RAY DIFFRACTIONf_dihedral_angle_d16.955239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.32781440.3232422X-RAY DIFFRACTION99.69
1.94-2.130.22981160.23182473X-RAY DIFFRACTION100
2.13-2.440.29961350.23452476X-RAY DIFFRACTION99.96
2.44-3.080.22731200.25822525X-RAY DIFFRACTION99.96
3.08-30.990.26051280.23962696X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 39.0320284698 Å / Origin y: -9.42510633136 Å / Origin z: -20.7102257922 Å
111213212223313233
T0.186429689011 Å2-0.0704086731039 Å2-0.059131407361 Å2-0.242925681218 Å20.00109696352517 Å2--0.243281406927 Å2
L0.72869577758 °2-0.217548276057 °2-1.31050133959 °2-0.694281966065 °2-0.403162677445 °2--2.82642258975 °2
S-0.0536155620451 Å °-0.182648833965 Å °-0.100609568237 Å °0.0512280267434 Å °-0.0394732667968 Å °-0.0350136554355 Å °0.156726132334 Å °0.438714615975 Å °0.0275039584052 Å °
Refinement TLS groupSelection details: chain 'A'

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