8fvq

PCSK9 in complex with an inhibitor

Method: X-RAY DIFFRACTION D_max: 81.3 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proprotein convertase subtilisin/kexin type 9

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–152 Chain B； UniProt 153–692	Fragment：prodomain residues 1-152	ACE-PHE-VAL-DAB-THR-THR-PHE-MAA-BIF-YBR inhibitor × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；20.0% Peg-6000, 0.1M Tris pH8.0	Resolution 2.57 Å R-free 0.260

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8FVQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10SB PCSK9 in complex with cyclic peptide 21 Deposited 2026-02-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 31–152（122 aa） Chain B 153–452（300 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.83 Å R-free 0.238
2P4E Crystal Structure of PCSK9 Deposited 2007-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain P 1–692（692 aa）	Not recorded	HG MERCURY (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；300 K；25% PEG 1500, 50 mM Tris-HCl buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.98 Å R-free 0.250
2P4E Crystal Structure of PCSK9 Deposited 2007-03-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–692（692 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；300 K；25% PEG 1500, 50 mM Tris-HCl buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.98 Å R-free 0.250
2P4E Crystal Structure of PCSK9 Deposited 2007-03-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–692（692 aa） Chain P 1–692（692 aa）	Not recorded	HG MERCURY (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；300 K；25% PEG 1500, 50 mM Tris-HCl buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.98 Å R-free 0.250
2QTW The Crystal Structure of PCSK9 at 1.9 Angstroms Resolution Reveals structural homology to Resistin within the C-terminal domain Deposited 2007-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–152（124 aa） Fragment：UNP residues 29-152 Chain B 153–692（540 aa） Fragment：UNP residues 153-692	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.5；298 K；20% PEG6000, 0.2M sodium chloride, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 10.50	Resolution 1.90 Å R-free 0.239
2W2M WT PCSK9-DELTAC BOUND TO WT EGF-A OF LDLR Deposited 2008-11-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 153–451（299 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 153-451 Chain P 53–152（100 aa） Fragment：PROPEPTIDE, RESIDUES 53-152	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 10% (V/V) 2-PROPANOL, 20% (W/V) PEG 4000	Resolution 2.40 Å R-free 0.254
2W2N WT PCSK9-deltaC bound to EGF-A H306Y mutant of LDLR Deposited 2008-11-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 153–451（299 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 153-451 Chain P 53–152（100 aa） Fragment：PRODOMAIN, RESIDUES 53-152	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 10% (W/V) PEG 8000, 8% (V/V) ETHYLENE GLYCOL.	Resolution 2.30 Å R-free 0.254
2W2O PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR Deposited 2008-11-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 153–451（299 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 153-451 Chain P 53–152（100 aa） Fragment：PROPEPTIDE, RESIDUES 53-152	Mutation：YES	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 10% (W/V) PEG 8000 AND 8% (V/V) ETHYLENE GLYCOL	Resolution 2.62 Å R-free 0.263
2W2P PCSK9-deltaC D374A mutant bound to WT EGF-A of LDLR Deposited 2008-11-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 153–451（299 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 153-451 Chain P 53–152（100 aa） Fragment：PRODOMAIN, RESIDUES 53-152	Mutation：YES	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 10% (W/V) PEG 8000 AND 8% (V/V) ETHYLENE GLYCOL	Resolution 2.62 Å R-free 0.270
2W2Q PCSK9-deltaC D374H mutant bound to WT EGF-A of LDLR Deposited 2008-11-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 153–451（299 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 153-451 Chain P 53–152（100 aa） Fragment：PROPEPTIDE, RESIDUES 53-152	Mutation：YES	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1M HEPES PH 7.5, 10% (W/V) PEG 8000 AND 8% (V/V) ETHYLENE GLYCOL	Resolution 2.33 Å R-free 0.253
2XTJ The crystal structure of PCSK9 in complex with 1D05 Fab Deposited 2010-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 153–451（299 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 153-451 Chain P 53–152（100 aa） Fragment：PRODOMAIN, RESIDUES 53-152	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；CRYSTALLIZATION EXPERIMENTS WERE PERFORMED AT ROOM TEMPERATURE BY THE HANGING-DROP AND SITTING-DROP METHODS. THIN PLATE-LIKE CRYSTALS WERE OBTAINED IN 100 MM NA CITRATE PH 6.5, 13% PEG 6000. FOR DATA COLLECTION CRYSTALS WERE TRANSFERRED TO A STABILIZING SOLUTION (20 MM TRIS PH 8.0, 50 MM NACITRATE PH 6.5, 100 MM NACL, 5% GLYCEROL, 1 MM TCEP, 1 MICROM CACL2, 25% PEG6000), THEN TRANSFERRED FOR 2 MIN TO A CRYOPROTECTANT SOLUTION (20 MM TRIS PH 8.0, 50 MM NACITRATE PH 6.5, 100 MM NACL, 20% GLYCEROL, 1 MM TCEP, 1 MICROM CACL2, 35% PEG6000) AND FINALLY PLACED DIRECTLY INTO LIQUID NITROGEN.	Resolution 2.70 Å R-free 0.259
3BPS PCSK9:EGF-A complex Deposited 2007-12-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 153–692（540 aa） Fragment：Catalytic domain, UNP residues 153-692 Chain P 53–152（100 aa） Fragment：Prodomain, UNP residues 53-152	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；294 K；0.3M (NH4)H2PO4, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 4.80	Resolution 2.41 Å R-free 0.240
3GCW PCSK9:EGFA(H306Y) Deposited 2009-02-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 153–692（540 aa） Chain P 53–152（100 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；294 K；0.3M (NH4)H2PO4, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.70 Å R-free 0.278
3GCX PCSK9:EGFA (pH 7.4) Deposited 2009-02-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 153–692（540 aa） Chain P 53–152（100 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；294 K；0.3M (NH4)H2PO4, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.70 Å R-free 0.261
3H42 Crystal structure of PCSK9 in complex with Fab from LDLR competitive antibody Deposited 2009-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 31–152（122 aa） Fragment：UNP residues 31-152 Chain B 153–692（540 aa） Fragment：UNP residues 153-692	Mutation：N533A	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；293 K；0.1 M Tris-HCl, 0.2 M Sodium acetate, 10-15% PEG 4000, 3-6% Dextran sodium salt (Mr 5000), pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.209
3M0C The X-ray Crystal Structure of PCSK9 in Complex with the LDL receptor Deposited 2010-03-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 29–152（124 aa） Fragment：PCSK9 Chain B 153–692（540 aa） Fragment：PCSK9	Mutation：D374Y	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；297 K；1.4 M Ammonium phosphate, 0.2M sodium chloride in 0.1M Imidazole buffer, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 7.01 Å R-free 0.362
3P5B The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation Deposited 2010-10-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 153–692（540 aa） Chain P 61–152（92 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；0.1 M sodium cacodylate pH 7.0, 1.7 M sodium acetate, 300 mM NaCl, 5% ethanol, VAPOR DIFFUSION, temperature 291K	Resolution 3.30 Å R-free 0.298
3P5C The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation Deposited 2010-10-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 153–692（540 aa） Chain P 61–152（92 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；0.1M imidazole, 0.7M sodium acetate pH 7.0, VAPOR DIFFUSION, temperature 291K	Resolution 4.20 Å R-free 0.348
3SQO PCSK9 J16 Fab complex Deposited 2011-07-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 153–692（540 aa） Chain P 31–152（122 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；7% PEG 10000, 100 mM Hepes pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.283
4K8R An Antibody Against the C-terminal Domain of PCSK9 lowers LDL Cholesterol Levels in vivo Deposited 2013-04-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 61–152（92 aa） Fragment：unp residues 61-152 Chain B 153–692（540 aa） Fragment：unp residues 153-692	Mutation：V474I, G670E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.5 M lithium sulfate, 0.1 M disodium malonate, 11.5 % PEG 8K , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.22 Å R-free 0.226
4NE9 PCSK9 in complex with LDLR peptide Deposited 2013-10-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 153–692（540 aa） Fragment：UNP residues 153-692 Chain P 1–152（152 aa） Fragment：UNP residues 1-152	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；299 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K	Resolution 2.60 Å R-free 0.211
4NE9 PCSK9 in complex with LDLR peptide Deposited 2013-10-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 153–692（540 aa） Fragment：UNP residues 153-692 Chain C 1–152（152 aa） Fragment：UNP residues 1-152	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；299 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K	Resolution 2.60 Å R-free 0.211
4NMX PCSK9(deltaCRD) in complex with phage-derived inhibitory peptide 2-8 Deposited 2013-11-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 31–152（122 aa） Fragment：propeptide (UNP residues 31-152) Chain B 153–452（300 aa） Fragment：catalytic domain (UNP residues 153-452)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M lithium chloride, 10% w/v PEG6000, 0.05 M Tris, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.85 Å R-free 0.222
4OV6 Crystal structure of PCSK9(53-451) with Adnectin Deposited 2014-02-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 60–152（93 aa） Fragment：prodomain (UNP residues 60-152) Chain B 153–446（294 aa） Fragment：catalytic domain (UNP residues 153-446)	Not recorded	EDO 1,2-ETHANEDIOL × 3 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；22% v/v PEG200, 1% v/v ethylene glycol, 0.1 M MES pH 6.5, crystals harvested next day, cryo-protectant: 30% v/v PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.69 Å R-free 0.231
4OV6 Crystal structure of PCSK9(53-451) with Adnectin Deposited 2014-02-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 60–152（93 aa） Fragment：prodomain (UNP residues 60-152) Chain E 153–446（294 aa） Fragment：catalytic domain (UNP residues 153-446)	Not recorded	EDO 1,2-ETHANEDIOL × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；22% v/v PEG200, 1% v/v ethylene glycol, 0.1 M MES pH 6.5, crystals harvested next day, cryo-protectant: 30% v/v PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.69 Å R-free 0.231
5OCA PCSK9:Fab Complex with Dextran Sulfate Deposited 2017-06-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 31–152（122 aa） Chain B 153–692（540 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；293 K；0.1 M Tris-HCl, 0.2 M Sodium acetate, 10-15% PEG 4000, 3-6% Dextran sodium salt (Mr 5000), pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.195
5VL7 PCSK9 complex with Fab33 Deposited 2017-04-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–152（152 aa） Fragment：prodomain residues 1-152 Chain B 153–692（540 aa） Fragment：catalytic and cysteine-rich domains, residues 153-692	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；potassium sodium phosphate	Resolution 3.50 Å R-free 0.245
5VLA Short PCSK9 delta-P' complex with Fusion2 peptide Deposited 2017-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–452（452 aa） Fragment：residues 1-452	Mutation：R165S	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；calcium acetate, PEG 6000	Resolution 2.40 Å R-free 0.267
5VLH Short PCSK9 delta-P' complex with peptide Pep1 Deposited 2017-04-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–452（452 aa） Fragment：residues 1-452	Mutation：R165S	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；calcium acetate, PEG 6000	Resolution 2.86 Å R-free 0.253
5VLK Short PCSK9 delta-P' complex with shrunken peptide bearing homo-Arginine Deposited 2017-04-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–452（452 aa） Fragment：residues 1-452	Mutation：R165S	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；calcium acetate, PEG 6000	Resolution 2.20 Å R-free 0.237
5VLL Short PCSK9 delta-P' complex with peptide Pep3 Deposited 2017-04-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–452（452 aa） Fragment：residues 1-452	Mutation：R165S	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；calcium acetate, PEG 6000	Resolution 2.37 Å R-free 0.244
5VLP PCSK9 complex with LDLR antagonist peptide and Fab7G7 Deposited 2017-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–692（692 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；ammonium acetate, 1,8diaminooctane	Resolution 2.90 Å R-free 0.209
6E4Y Anti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9, unmodified Deposited 2018-07-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 32–53（22 aa） Fragment：UNP residues 32-53	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；15% w/v PEG8000, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.5	Resolution 2.24 Å R-free 0.255
6E4Z Anti-PCSK9 fab 6E2 bound to the modified N-terminal peptide from PCSK9 Deposited 2018-07-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 32–53（22 aa） Fragment：UNP residues 32-53	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；15% w/v PEG8000, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.5	Resolution 2.20 Å R-free 0.236
6MV5 Anti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9 (E32K) Deposited 2018-10-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 32–53（22 aa） Fragment：N-terminal peptide (UNP residues 32-53)	Mutation：E32K Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 CL CHLORIDE ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；15% PEG8000, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.5	Resolution 2.10 Å R-free 0.238
6OLZ Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNA Deposited 2019-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric	Chain A 9–34（26 aa）	Not recorded	MG MAGNESIUM ION × 326 ZN ZINC ION × 5 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6OM0 Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with AP and PE tRNAs Deposited 2019-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric	Chain y 9–34（26 aa）	Not recorded	MG MAGNESIUM ION × 31 ZN ZINC ION × 6 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6OM7 Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like small molecule with AA and PE tRNAs Deposited 2019-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric	Chain y 9–34（26 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 31 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6U26 PCSK9 in complex with compound 16 Deposited 2019-08-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–692（662 aa）	Mutation：V474I, G670E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris (pH 7.8) 200 mM NaCl, 15% PEG 3350,	Resolution 1.53 Å R-free 0.213
6U26 PCSK9 in complex with compound 16 Deposited 2019-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 31–692（662 aa）	Mutation：V474I, G670E	063 4'-{[(1R)-6-{2-[2-({N~5~-[N,N'-bis(tert-butoxycarbonyl)carbamimidoyl]-N~2~-(tert-butoxycarbonyl)-L-ornithyl}amino)ethoxy]ethoxy}-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}-2'-fluoro[1,1'-biphenyl]-4-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris (pH 7.8) 200 mM NaCl, 15% PEG 3350,	Resolution 1.53 Å R-free 0.213
6U2F PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)IGLLR - NH2 Deposited 2019-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–692（692 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；4 M ammonium acetate, 0.1 M Tris, pH 8.5, 3% v/v 1,8 diaminooctane	Resolution 2.94 Å R-free 0.209
6U2N PCSK9 in complex with compound 4 Deposited 2019-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–692（662 aa） Chain B 31–692（662 aa）	Not recorded	PV7 4-{[(1R)-6-methoxy-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；303 K；(10-22)% PEG 10000, 0.1M Tris, pH 8.5, 10% Ethylene Glycol, 1% BAM	Resolution 2.15 Å R-free 0.234
6U2P PCSK9 in complex with compound 5 Deposited 2019-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–692（662 aa） Chain B 31–692（662 aa）	Mutation：V474I, G670E Mutation：V474I, G670E	EDO 1,2-ETHANEDIOL × 5 PUV 2-fluoro-4-{[(1R)-6-methoxy-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；303 K；(10-22)% PEG 10000, 0.1M Tris, pH 8.5, 10% Ethylene Glycol, 1% BAM	Resolution 2.04 Å R-free 0.216
6U36 PCSK9 in complex with a Fab and compound 14 Deposited 2019-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 31–692（662 aa） Chain B 31–692（662 aa）	Mutation：V474I, G670E Mutation：V474I, G670E	PVM 2-fluoro-4-{[(1R)-6-(2-{4-[1-(4-methoxyphenyl)-5-methyl-6-oxo-1,6-dihydropyridazin-3-yl]-1H-1,2,3-triazol-1-yl}ethoxy)-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1M Bicine pH9.0, 2% dioxane, 10% PEG 20000	Resolution 2.70 Å R-free 0.251
6U38 PCSK9 in complex with a Fab and compound 8 Deposited 2019-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 31–692（662 aa） Chain B 31–692（662 aa）	Mutation：V474I, G670E Mutation：V474I, G670E	PVJ 2-fluoro-4-{[(1R)-1-methyl-6-{[(2S)-oxan-2-yl]methoxy}-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1M Bicine pH9.0, 2% dioxane, 10% PEG 20000	Resolution 2.73 Å R-free 0.243
6U3I Design of organo-peptides as bipartite PCSK9 antagonists Deposited 2019-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–692（692 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；4 M ammonium acetate, 0.1 M Tris, pH 8.5, 3% v/v 1,8 diaminooctane	Resolution 2.90 Å R-free 0.217
6U3X PCSK9 in complex with compound 2 Deposited 2019-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–692（662 aa） Chain B 31–692（662 aa）	Mutation：V474I, G670E Mutation：V474I, G670E	PVV 2-[(1R)-6,7-dimethoxy-1-methyl-1,2,3,4-tetrahydroisoquinolin-1-yl]-N-(1,3-thiazol-2-yl)acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；303 K；10-22% PEG 10K, 0.1M Tris, pH 8.5, 10% ethylene glycol, 1% BAM	Resolution 2.64 Å R-free 0.284
6XIB PCSK9(deltaCRD) in complex with cyclic peptide 30 Deposited 2020-06-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 31–152（122 aa） Chain B 153–452（300 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；20% PEG3350, 200mM CaCl2, 100mM MES pH 6	Resolution 1.55 Å R-free 0.205
6XIC PCSK9(deltaCRD) in complex with cyclic peptide 40 Deposited 2020-06-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 32–152（121 aa） Chain B 153–452（300 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；20% PEG3350, 200mM CaCl2, 100mM MES pH 6	Resolution 1.38 Å R-free 0.221
6XID PCSK9(deltaCRD) in complex with cyclic peptide 51 Deposited 2020-06-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 31–152（122 aa） Chain B 153–452（300 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；20% PEG3350, 200mM CaCl2, 100mM MES pH 6	Resolution 1.48 Å R-free 0.205
6XIE PCSK9(deltaCRD) in complex with cyclic peptide 77 Deposited 2020-06-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 31–152（122 aa） Chain B 153–452（300 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；20% PEG3350, 200mM CaCl2, 100mM MES pH 6	Resolution 1.43 Å R-free 0.221
6XIF PCSK9(deltaCRD) in complex with cyclic peptide 83 Deposited 2020-06-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 31–152（122 aa） Chain B 153–452（300 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；20% PEG3350, 200mM CaCl2, 100mM MES pH 6	Resolution 1.77 Å R-free 0.204
7ANQ Complete PCSK9 C-ter domain in complex with VHH P1.40 Deposited 2020-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 452–682（231 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Protein: Purified PCSK9/P1.40 complex at 5.3 mg/ml Precipitant: 10% PEG 4.000, 0.2M imidazole malate, pH 7.0 Cryoprotectant: 40% SM3 (25 % diethylene glycol + 25 % ethylene glycol + 25 % glycerol + 25 % 1,4-dioxane) 25% PEG 4.000, 0.2M imidazole malate, pH 7.0	Resolution 2.20 Å R-free 0.256
7KEV PCSK9 in complex with a cyclic peptide LDLR disruptor Deposited 2020-10-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 29–152（124 aa） Chain B 153–692（540 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20.0% PEG-6000, 0.1M TRIS	Resolution 2.80 Å R-free 0.280
7KFA PCSK9 in complex with PCSK9i a 13mer cyclic peptide LDLR disruptor Deposited 2020-10-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 29–152（124 aa） Chain B 153–692（540 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20.0% PEG-6000, 0.1M TRIS	Resolution 2.45 Å R-free 0.242
7S5G PCSK9 in complex with compound 19 Deposited 2021-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 31–152（122 aa） Chain B 153–452（300 aa）	Not recorded	GOL GLYCEROL × 1 89N (2E)-but-2-ene-1,4-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；20% PEG3350, 200mM CaCl2, 100mM MES pH 6	Resolution 2.04 Å R-free 0.286
7S5H PCSK9(deltaCRD) in complex with cyclic peptide 35 Deposited 2021-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 31–152（122 aa） Chain B 153–452（300 aa）	Not recorded	89N (2E)-but-2-ene-1,4-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；20% PEG3350, 200mM CaCl2, 100mM MES pH 6	Resolution 1.27 Å R-free 0.209
8FPO PCSK9 in complex with an inhibitor Deposited 2023-01-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–152（152 aa） Fragment：prodomain residues 1-152 Chain B 153–692（540 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris-HCl (pH 8.0), 14-19% PEG 6000	Resolution 3.00 Å R-free 0.250
8FPQ PCSK9 in complex with an inhibitor Deposited 2023-01-05	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 61–152（92 aa） Chain B 153–682（530 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20.0% Peg-6000, 0.1M Tris pH8.0	Resolution 2.50 Å R-free 0.234
8FVL PCSK9 in complex with an inhibitor Deposited 2023-01-19	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–152（152 aa） Fragment：prodomain residues 1-152 Chain B 153–692（540 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20.0% Peg-6000, 0.1M Tris pH8.0	Resolution 1.96 Å R-free 0.218
8FVM PCSK9 in complex with an inhibitor Deposited 2023-01-19	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–152（152 aa） Chain B 153–692（540 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20.0% Peg-6000, 0.1M Tris pH8.0	Resolution 2.85 Å R-free 0.238
8FVN PCSK9 in complex with an inhibitor Deposited 2023-01-19	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–152（152 aa） Fragment：prodomain residues 1-152 Chain B 153–692（540 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20.0% Peg-6000, 0.1M Tris pH8.0	Resolution 2.71 Å R-free 0.257
8FVO PCSK9 in complex with an inhibitor Deposited 2023-01-19	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–152（152 aa） Fragment：prodomain residues 1-152 Chain B 153–692（540 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20.0% Peg-6000, 0.1M Tris pH8.0	Resolution 2.65 Å R-free 0.239
8FVP PCSK9 in complex with an inhibitor Deposited 2023-01-19	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–152（152 aa） Fragment：prodomain residues 1-152 Chain B 153–692（540 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20.0% Peg-6000, 0.1M Tris pH8.0	Resolution 2.60 Å R-free 0.215
8VDV pcsk9 in complex with inhibitor Deposited 2023-12-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 61–152（92 aa） Fragment：PRODOMAIN, UNP RESIDUES 1-152 Chain B 153–681（529 aa） Fragment：UNP RESIDUES 153-692	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；298 K；20.0% Peg-6000, 0.1M Tris pH8.0	Resolution 1.97 Å R-free 0.217
8WFR The Crystal Structure of PCSK9 from Biortus. Deposited 2023-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–152（122 aa） Chain B 153–692（540 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M HEPES pH7.5, 20% PEG 10000	Resolution 1.95 Å R-free 0.203
9HZ3 PCSK9 AZD0780 complex Deposited 2025-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–152（152 aa） Chain B 153–692（540 aa）	Not recorded	A1IYR 1-[6-[[(1~{S},3~{S})-3-[[5-[bis(fluoranyl)methoxy]pyrimidin-2-yl]amino]cyclopentyl]amino]pyridin-3-yl]pyridin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；25 mM HEPES pH 7.5 300 mM NaCl 5% glycerol	Resolution 1.43 Å R-free 0.213
9SZY PCSK9 CTD fragment structure Deposited 2025-10-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–152（152 aa） Chain B 1–692（692 aa）	Not recorded	A1JSM ~{N}-(2-methylpropyl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25 mM HEPES pH 7.5 300 mM NaCl 5% glycerol	Resolution 1.76 Å R-free 0.236

63 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PCSK9_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–152； UniProt 1–152 Author chain B； PDBConstruct 1–540； UniProt 153–692

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8fvq
Deposition date deposition_date	2023-01-19
Structure title title	PCSK9 in complex with an inhibitor
Keywords keywords	complex, inhibitor, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.21 Å
Radius of gyration Rg (electron density) rg_electron	25.13 Å
Forward intensity I(0) i0	68047900.00
Molecular weight molecular_weight	62259.0 kDa
Excluded volume excluded_volume	77142 Å³
Envelope volume envelope_volume	94688 Å³
Hydration-shell volume shell_volume	30960 Å³
Envelope diameter envelope_diameter	84.1 Å
Shell Rg shell_rg	32.93 Å
Envelope Rg envelope_rg	25.34 Å
Shape Rg shape_rg	25.12 Å
Total Rg total_rg	25.98 Å
Total atoms total_atoms	4363
Residues n_residues	574
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	81.3 Å
Rg (real space) rg_real	26.13 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	6.8050e+07
I(0) uncertainty (real space) i0_real_error	8.9950e+05
Rg (reciprocal space) rg_reciprocal	26.16 Å
I(0) (reciprocal space) i0_reciprocal	68050000.0000
Solution quality estimate total_estimate	0.9099
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	80.0 Å
Skewness Skewness skewness	0.218
Kurtosis Kurtosis kurtosis	-0.545
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15230000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.968

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Proprotein convertase subtilisin/kexin type 9
Molecular weight formula_weight	17035.5 kDa
EC 编号 ec_number	3.4.21.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4400

MGTVSSRRSWWPLPLLLLLLLLLGPAGARAQEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Proprotein convertase subtilisin/kexin type 9
Molecular weight formula_weight	57443.7 kDa
EC 编号 ec_number	3.4.21.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEEAVTAVAICCRSRHLAQASQELQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	ACE-PHE-VAL-DAB-THR-THR-PHE-MAA-BIF-YBR inhibitor
Molecular weight formula_weight	1191.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

XFVATTFAFX

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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8. Citations (1)

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Unit-cell length a length_a	71.300 Å
Unit-cell length b length_b	150.593 Å
Unit-cell length c length_c	63.541 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.570 Å
Low-resolution limit resolution_low	58.540 Å
R factor r_factor	0.2041
R_work r_work	0.2011
R_free r_free	0.2601

fit	/app/data/saxs_computation/fv/8fvq/8fvq.fit
pddf	/app/data/pr_computation/fv/8fvq/8fvq.pr.out
profile	/app/data/saxs_computation/fv/8fvq/8fvq.dat

PCSK9 in complex with an inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Proprotein convertase subtilisin/kexin type 9

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)