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- PDB-9q8k: Synthetic bicyclic peptide -

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Basic information

Entry
Database: PDB / ID: 9q8k
TitleSynthetic bicyclic peptide
ComponentsSynthetic bicyclic peptide (CYS-SER-ASP-ALA-LEU-CYS-LYS-PHE-PHE-ARG-GLU-ASN-THR-LYS-CYS)
KeywordsDE NOVO PROTEIN / peptide inhibitor
Function / homologyChem-LFI
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsXue, Y. / Ek, M. / Sandmark, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other private Sweden
CitationJournal: To Be Published
Title: Structure of GFRaL-peptide complex
Authors: Sandmark, J. / Xue, Y. / Ek, M.
History
DepositionFeb 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synthetic bicyclic peptide (CYS-SER-ASP-ALA-LEU-CYS-LYS-PHE-PHE-ARG-GLU-ASN-THR-LYS-CYS)
B: Synthetic bicyclic peptide (CYS-SER-ASP-ALA-LEU-CYS-LYS-PHE-PHE-ARG-GLU-ASN-THR-LYS-CYS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5684
Polymers3,5842
Non-polymers9842
Water45025
1
A: Synthetic bicyclic peptide (CYS-SER-ASP-ALA-LEU-CYS-LYS-PHE-PHE-ARG-GLU-ASN-THR-LYS-CYS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2842
Polymers1,7921
Non-polymers4921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Synthetic bicyclic peptide (CYS-SER-ASP-ALA-LEU-CYS-LYS-PHE-PHE-ARG-GLU-ASN-THR-LYS-CYS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2842
Polymers1,7921
Non-polymers4921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.720, 82.720, 82.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein/peptide Synthetic bicyclic peptide (CYS-SER-ASP-ALA-LEU-CYS-LYS-PHE-PHE-ARG-GLU-ASN-THR-LYS-CYS)


Mass: 1792.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-LFI / 1-[3,5-bis(3-bromanylpropanoyl)-1,3,5-triazinan-1-yl]-3-bromanyl-propan-1-one / Chemical crosslinker


Mass: 492.002 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18Br3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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

Crystal growTemperature: 298 K / Method: evaporation / Details: 25 mM Hepes pH 7.5, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS MYTHEN2 X 1K / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.67→41.36 Å / Num. obs: 11097 / % possible obs: 100 % / Redundancy: 39.8 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.011 / Rrim(I) all: 0.067 / Χ2: 0.82 / Net I/σ(I): 30.6 / Num. measured all: 441916
Reflection shellResolution: 1.67→1.71 Å / % possible obs: 100 % / Redundancy: 40.6 % / Rmerge(I) obs: 2.399 / Num. measured all: 33603 / Num. unique obs: 828 / CC1/2: 0.647 / Rpim(I) all: 0.38 / Rrim(I) all: 2.429 / Χ2: 0.42 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
BUSTER2.11.7 PACIOREKrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→41.36 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.072 / SU Rfree Blow DPI: 0.075 / SU Rfree Cruickshank DPI: 0.072
RfactorNum. reflection% reflectionSelection details
Rfree0.262 526 4.74 %RANDOM
Rwork0.235 ---
obs0.236 11092 100 %-
Displacement parametersBiso mean: 41.14 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.67→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms240 0 42 25 307
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01290HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13376HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d98SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes50HARMONIC5
X-RAY DIFFRACTIONt_it290HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion16.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion32SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact330SEMIHARMONIC4
LS refinement shellResolution: 1.67→1.69 Å / Total num. of bins used: 26
RfactorNum. reflection% reflection
Rfree0.2006 -5.15 %
Rwork0.2225 405 -
all0.2214 427 -
obs--100 %

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