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

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Basic information

Entry
Database: PDB / ID: 9tlp
TitleDe novo designed single-chain antiparallel coiled-coil hairpin with binding site for BCL-xL, Sc-apCC-2-BCL-xL-6
ComponentsSc-apCC-2-BCL-xL-6
KeywordsDE NOVO PROTEIN / Protein Binder / Computational Design / Coiled-coil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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-6
B: Sc-apCC-2-BCL-xL-6
C: Sc-apCC-2-BCL-xL-6
D: Sc-apCC-2-BCL-xL-6


Theoretical massNumber of molelcules
Total (without water)34,3844
Polymers34,3844
Non-polymers00
Water5,981332
1
A: Sc-apCC-2-BCL-xL-6


Theoretical massNumber of molelcules
Total (without water)8,5961
Polymers8,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sc-apCC-2-BCL-xL-6


Theoretical massNumber of molelcules
Total (without water)8,5961
Polymers8,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sc-apCC-2-BCL-xL-6


Theoretical massNumber of molelcules
Total (without water)8,5961
Polymers8,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sc-apCC-2-BCL-xL-6


Theoretical massNumber of molelcules
Total (without water)8,5961
Polymers8,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.211, 46.110, 54.103
Angle α, β, γ (deg.)90.510, 96.519, 106.022
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Sc-apCC-2-BCL-xL-6


Mass: 8595.909 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.03 M Sodium nitrate, 0.03 M Sodium phosphate dibasic, 0.03 M Ammonium sulphate, 0.01 M HEPES, 0.01 MOPS, 20% v/v PEG 500 MME; 10% w/v PEG 20000

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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: 1.75→33.48 Å / Num. obs: 26841 / % possible obs: 98.78 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 1 / Net I/σ(I): 20.24
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 2646 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→33.48 Å / SU ML: 0.1845 / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 19.3745
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2013 1337 4.98 %
Rwork0.1542 25497 -
obs0.1565 26834 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.92 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 0 332 2646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662377
X-RAY DIFFRACTIONf_angle_d0.81993193
X-RAY DIFFRACTIONf_chiral_restr0.0427360
X-RAY DIFFRACTIONf_plane_restr0.008423
X-RAY DIFFRACTIONf_dihedral_angle_d14.0034942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.25061230.18692523X-RAY DIFFRACTION96.99
1.81-1.890.22411280.16792514X-RAY DIFFRACTION98.44
1.89-1.970.23221400.16232568X-RAY DIFFRACTION98.47
1.97-2.070.21411500.15382544X-RAY DIFFRACTION98.75
2.07-2.20.18961370.14382531X-RAY DIFFRACTION98.89
2.2-2.370.17711250.14022552X-RAY DIFFRACTION99
2.37-2.610.20111200.14892578X-RAY DIFFRACTION99.05
2.61-2.990.20641390.162557X-RAY DIFFRACTION99.26
2.99-3.770.18581560.15192540X-RAY DIFFRACTION99.37
3.77-33.480.20221190.15462590X-RAY DIFFRACTION99.63
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)
11.035764984390.716535214904-1.371291612561.47819299969-2.184889605774.683506591780.0458676132845-0.06326835477750.07490643474930.0715733643342-0.02681721258390.0379396037703-0.04945370064160.0990385778145-0.01466597696370.05483542960050.0162346757537-0.0009226677412280.0384966206223-0.01922600758720.077856678022312.73977282823.999036652941.78522855265
21.761975598111.02236473613-2.082173552922.61898303064-2.711947633585.13009182840.05240630803730.08110111308410.229053202724-0.07402751051440.05195531258690.0452098525954-0.0827259565059-0.037445310982-0.1102772467210.04794103950450.00722736548854-0.03137867544650.0943299215310.01434269079240.1308933042914.98485564612.830160777-15.3523839603
32.250289358940.0916300147961.752572502541.34136312139-0.4955074254463.257925524930.08459258847930.0368854843233-0.209651923938-0.01916891334180.0625732211491-0.008576110879070.119073368550.00220809470158-0.156833505040.06664214499530.008308121932430.03885079684680.044261950202-0.01065997380130.089257850545610.8078773425-12.3018502114-1.37835081687
41.6188228323-0.7797976277321.478794479180.986201378446-1.096727794443.111251139170.1269945498950.0842522995502-0.210415561674-0.06569313384560.04098272025770.1205888838080.1605485005950.130934028958-0.1655621731690.0752194161303-0.01748973830740.01948314440810.0639408619297-0.0274376302930.088325622398420.9241013283-9.76768274376-8.79825119375
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1 - 73

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain 'A'AA2 - 74
22chain 'B'BB1 - 73
33chain 'C'CC2 - 74
44chain 'D'DD3 - 75

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