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- PDB-10sb: PCSK9 in complex with cyclic peptide 21 -

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Basic information

Entry
Database: PDB / ID: 10sb
TitlePCSK9 in complex with cyclic peptide 21
Components
  • Cyclic peptide 21
  • Propeptide of Proprotein convertase subtilisin/kexin type 9
  • Proprotein convertase subtilisin/kexin type 9
KeywordsHYDROLASE / CHOLESTEROL / LDL RECEPTOR / EGFA DOMAIN
Function / homology
Function and homology information


low-density lipoprotein particle receptor catabolic process / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / negative regulation of sodium ion import across plasma membrane / PCSK9-LDLR complex / PCSK9-AnxA2 complex / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / positive regulation of low-density lipoprotein particle receptor catabolic process ...low-density lipoprotein particle receptor catabolic process / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / negative regulation of sodium ion import across plasma membrane / PCSK9-LDLR complex / PCSK9-AnxA2 complex / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / positive regulation of low-density lipoprotein particle receptor catabolic process / low-density lipoprotein particle binding / LDL clearance / lipoprotein metabolic process / very-low-density lipoprotein particle receptor binding / transporter inhibitor activity / signaling receptor inhibitor activity / negative regulation of receptor internalization / COPII-coated ER to Golgi transport vesicle / sodium channel inhibitor activity / endolysosome membrane / negative regulation of low-density lipoprotein particle clearance / lysosomal transport / triglyceride metabolic process / low-density lipoprotein particle receptor binding / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of receptor internalization / apolipoprotein binding / cholesterol metabolic process / phospholipid metabolic process / neurogenesis / regulation of neuron apoptotic process / cholesterol homeostasis / cellular response to starvation / VLDLR internalisation and degradation / Post-translational protein phosphorylation / kidney development / liver development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron differentiation / cellular response to insulin stimulus / late endosome / positive regulation of neuron apoptotic process / endopeptidase activity / early endosome / lysosome / endoplasmic reticulum lumen / serine-type endopeptidase activity / lysosomal membrane / apoptotic process / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / Golgi apparatus / : / RNA binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily ...Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / : / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
: / GLYCOLIC ACID / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.828 Å
AuthorsOrth, P. / Hong, M.R. / Klein, D.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2026
Title: Discovery Process of Enlicitide, a Highly Engineered Macrocyclic Peptide Therapeutic, through Issue-Driven Fragment-Based Synthetic Assembly and SAR.
Authors: Josien, H. / Nair, A.G. / Ding, F.X. / Guo, Y. / Chen, Y.H. / Rao, A.U. / Liu, J. / Tong, L. / Sun, Z. / Lo, M.M. / Tucker, T.J. / Embrey, M.W. / Shahripour, A. / Wu, C. / Bianchi, E. / ...Authors: Josien, H. / Nair, A.G. / Ding, F.X. / Guo, Y. / Chen, Y.H. / Rao, A.U. / Liu, J. / Tong, L. / Sun, Z. / Lo, M.M. / Tucker, T.J. / Embrey, M.W. / Shahripour, A. / Wu, C. / Bianchi, E. / Branca, D. / Kuethe, J.T. / Lee, J. / Thaisrivongs, D.A. / Bulger, P.G. / Zhu, X. / Ha, S.N. / Johnston, J.M. / Klein, D.J. / Orth, P. / Hong, M.R. / Buevich, A.V. / Gao, Q. / Zokian, H.J. / Koeplinger, K.A. / Tracy, R.W. / Hafey, M.J. / Buist, N. / Bueters, T. / Alleyne, C. / Bass, A. / Campeau, L.C. / Johns, D.G. / Garbaccio, R.M. / Vachal, P. / Walji, A. / Wood, H.B.
History
DepositionFeb 4, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 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: Propeptide of Proprotein convertase subtilisin/kexin type 9
B: Proprotein convertase subtilisin/kexin type 9
D: Cyclic peptide 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1736
Polymers47,7713
Non-polymers4033
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-14 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.741, 70.741, 159.125
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Propeptide of Proprotein convertase subtilisin/kexin type 9


Mass: 13791.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Proprotein convertase subtilisin/kexin type 9 / Neural apoptosis-regulated convertase 1 / NARC-1 / Proprotein convertase 9 / PC9 / Subtilisin/kexin- ...Neural apoptosis-regulated convertase 1 / NARC-1 / Proprotein convertase 9 / PC9 / Subtilisin/kexin-like protease PC9


Mass: 32836.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCSK9, NARC1, PSEC0052 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Protein/peptide , 1 types, 1 molecules D

#3: Protein/peptide Cyclic peptide 21


Mass: 1142.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 256 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-A1C8P / N-{[4-(2-aminoethyl)phenyl]methyl}hexan-1-amine


Mass: 234.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 15% PEG3350, 200 mM magnesium acetate, 100 mM Tris (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.828→61.264 Å / Num. obs: 32915 / % possible obs: 78.9 % / Redundancy: 8.1 % / CC1/2: 0.991 / Net I/σ(I): 8.4
Reflection shellResolution: 1.828→1.974 Å / Redundancy: 6.9 % / Num. unique obs: 1646 / CC1/2: 0.39 / Net I/σ(I) obs: 1.2 / % possible all: 19.5

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.828→24.27 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1650 -RANDOM
Rwork0.1963 31238 --
obs0.1985 32888 78.9 %-
Displacement parametersBiso mean: 27.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.7801 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 1.828→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 107 253 3184
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083003HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994092HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1054SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes553HARMONIC8
X-RAY DIFFRACTIONt_it3003HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion393SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2736SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion15.63
LS refinement shellResolution: 1.83→1.94 Å
RfactorNum. reflection% reflection
Rfree0.3431 34 -
Rwork0.2917 624 -
obs0.2944 658 9.74 %

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