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

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Basic information

Entry
Database: PDB / ID: 9tlo
TitleDe novo designed single-chain antiparallel coiled-coil hairpin with binding site for BCL-xL, Sc-apCC-2-BCL-xL-5
ComponentsSc-apCC-2-BCL-xL-5
KeywordsDE NOVO PROTEIN / Protein Binder / Computational Design / Coiled-coil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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-BCL-xL-5
B: Sc-apCC-2-BCL-xL-5
C: Sc-apCC-2-BCL-xL-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8936
Polymers25,6163
Non-polymers2763
Water91951
1
A: Sc-apCC-2-BCL-xL-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6312
Polymers8,5391
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sc-apCC-2-BCL-xL-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7233
Polymers8,5391
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sc-apCC-2-BCL-xL-5


Theoretical massNumber of molelcules
Total (without water)8,5391
Polymers8,5391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.570, 69.570, 112.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

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Components

#1: Protein Sc-apCC-2-BCL-xL-5


Mass: 8538.833 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M Sodium citrate tribasic dihydrate, 0.1 M Sodium HEPES

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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: 2.2→45.09 Å / Num. obs: 38535 / % possible obs: 99.95 % / Redundancy: 26.3 % / Biso Wilson estimate: 37.54 Å2 / CC1/2: 1 / Net I/av σ(I): 13.06 / Net I/σ(I): 13.06
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 1417 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.09 Å / SU ML: 0.2158 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2474 765 5.21 %
Rwork0.2116 13909 -
obs0.2134 14674 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.74 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 18 51 1740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221706
X-RAY DIFFRACTIONf_angle_d0.36972294
X-RAY DIFFRACTIONf_chiral_restr0.0259268
X-RAY DIFFRACTIONf_plane_restr0.003297
X-RAY DIFFRACTIONf_dihedral_angle_d17.9862650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.27311510.23962716X-RAY DIFFRACTION100
2.37-2.610.27921390.21472733X-RAY DIFFRACTION100
2.61-2.990.29521740.22012721X-RAY DIFFRACTION99.97
2.99-3.760.23161460.20332792X-RAY DIFFRACTION100
3.76-45.090.22551550.20822947X-RAY DIFFRACTION99.81
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6821551660.4588387938650.8555199056062.991029045332.852390785997.536475185220.0404370270398-0.1667784837210.05577071142670.1868406511470.110328026969-0.0907569071710.199092827505-0.0646766856133-0.1645027786060.206617829074-0.002747791000640.05860775804550.1828343562430.04629732351420.239996145165-10.37749386854.78887499432-21.4562838079
21.217899922760.0635957526402-0.490843754265.19986196136-0.7896442500372.53544693465-0.0302722009730.0267002321292-0.0761800169328-0.378700225901-0.0474993518655-0.3699431412130.09203060723630.07599064754290.02558418782530.356146704663-0.005979147070610.04291539281770.270433868170.03786955469250.352466719301-11.7653930353-15.8179776387-24.184861087
32.303925438150.049590625086-1.743965134154.294326656411.783941542233.75061897854-0.09310102114020.2756579934820.282991370677-0.03356033872370.01565907267950.4707399568620.528544885879-0.5505452917770.1872278927940.328573251153-0.0616677341717-0.006911086378870.3000571368820.05519070057610.348100800162-24.2244655139-4.69041168238-20.9593249942
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A'AA2 - 741 - 73
22chain 'B'BB4 - 731 - 70
33chain 'C'CC1 - 731 - 73

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