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2w2p

PCSK9-deltaC D374A mutant bound to WT EGF-A of LDLR

Method: X-RAY DIFFRACTION Dmax: 89.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9

HOMO SAPIENS

UniProt Q8NBP7

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 153–451 Chain P； UniProt 53–152 Fragment：CATALYTIC DOMAIN, RESIDUES 153-451 Mutation：YES Fragment：PRODOMAIN, RESIDUES 53-152 LOW-DENSITY LIPOPROTEIN RECEPTOR × 1 （P01130） 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

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 2W2P 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 mutation/modification 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 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 ligand/ion 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 mutation/modification 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 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 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 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
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 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
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 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
2W2Q PCSK9-deltaC D374H mutant bound to WT EGF-A of LDLR Deposited 2008-11-03 Different construct Different ligand/ion 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 153–692（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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 153–692（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 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 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification 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 mutation/modification 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） 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 1–152（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 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 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 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 ligand/ion 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 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 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）
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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 construct Different mutation/modification 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 mutation/modification Different experimental conditions 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 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 1–152（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 mutation/modification Different experimental conditions 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 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 1–152（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 construct Different mutation/modification 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；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 construct Different mutation/modification 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；20.0% Peg-6000, 0.1M Tris pH8.0
Resolution 2.60 Å R-free 0.215
8FVQ PCSK9 in complex with an inhibitor Deposited 2023-01-19 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 1–152（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 2.57 Å R-free 0.260
8VDV pcsk9 in complex with inhibitor Deposited 2023-12-18 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 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 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 31–152（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 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 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 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 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, 3
Chains and sequence ranges Author chain A； PDBConstruct 1–299； UniProt 153–451 Author chain P； PDBConstruct 15–114； UniProt 53–152

LOW-DENSITY LIPOPROTEIN RECEPTOR

HOMO SAPIENS

UniProt P01130

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 E； UniProt 314–393 Fragment：EGF-A DOMAIN, RESIDUES 314-393 PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 × 1 （Q8NBP7） PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 × 1 （Q8NBP7） 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

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 2W2P Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AJJ LDL RECEPTOR LIGAND-BINDING MODULE 5, CALCIUM-COORDINATING Deposited 1997-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 196–232（37 aa） Fragment：LIGAND-BINDING DOMAIN, FIFTH REPEAT
Not recorded SO4 SULFATE ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLIZED FROM 2.1 M AMMONIUM SULFATE, PH 5.0, 25% SUCROSE
Resolution 1.70 Å R-free 0.240
1D2J LDL RECEPTOR LIGAND-BINDING MODULE 6 Deposited 1999-09-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 233–272（40 aa） Fragment：LIGAND-BINDING DOMAIN, SIXTH REPEAT
Mutation：M243L CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 5.2；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR measurement conditions pH 5.2；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR measurement conditions pH 5.2；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR measurement conditions pH 5.2；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR sample composition 1 MM LR6 U-15N; 10 MM CACL2
NMR sample composition 1 MM LR6 U-15N; 10 MM CACL2
NMR sample composition 1 MM LR6 UNLABELED; 10 MM CACL2
NMR sample composition 1 MM LR6 UNLABELED; 10 MM CACL2
Resolution not provided
1F5Y NMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-BINDING MODULES OF THE HUMAN LDL RECEPTOR Deposited 2000-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–104（83 aa） Fragment：LIGAND-BINDING MODULES 1-2
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 5.5；310 K；Ionic strength (raw mmCIF value) 0.045；Pressure atmospheric
NMR sample composition 1 mM LB1-2, 15 mM CaCl2, pH 5.5 | 95% H2O/5% D2O
NMR sample composition 1 mM LB1-2, 15 mM CaCl2, pH 5.5 | 99% D2O
Resolution not provided
1F8Z NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL RECEPTOR Deposited 2000-07-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 234–272（39 aa） Fragment：SIXTH LIGAND-BINDING MODULE
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1
NMR sample composition 3 mM LB6, 10 mM CaCl2, 1 mM 3,3,3-trimethylsilylpropionate | 90% H2O/10% D2O
NMR sample composition 3 mM LB6, 10 mM CaCl2, 1 mM 3,3,3-trimethylsilylpropionate | 100% D2O
Resolution not provided
1HJ7 NMR study of a pair of LDL receptor Ca2+ binding epidermal growth factor-like domains, 20 structures Deposited 2001-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 314–393（80 aa） Fragment：CA2+ BINDING EPIDERMAL GROWTH FACTOR-LIKE DOMAIN PAIR, RESIDUES 293-372
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) SEE REFERENCES
NMR sample composition SEE REFERENCES
Resolution not provided
1HZ8 SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR Deposited 2001-01-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 314–395（82 aa） Fragment：EGF-AB CONCATEMER (RESIDUES 314-395)
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 5.5；310 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR measurement conditions pH 5.5；283 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR measurement conditions pH 5.5；295 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR sample composition 1mM EGF-AB, 20mM CaCl2 | 95% H2O/5% D2O
NMR sample composition 1mM EGF-AB, 20mM CaCl2 | 99% D2O
NMR sample composition 1mM 15N-EGF-AB, 20mM CaCl2 | 95% H2O/5% D2O
NMR sample composition 1.5mM EGF-A, 20mM CaCl2 | 99% D2O
NMR sample composition 1.5mM EGF-A, 20mM CaCl2 | 95% H2O/5% D2O
Resolution not provided
1I0U SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF A CONCATEMER OF EGF-HOMOLOGY MODULES OF THE HUMAN LOW DENSITY LIPOPROTEIN RECEPTOR Deposited 2001-01-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 314–395（82 aa） Fragment：EGF-AB CONCATEMER(RESIDUES 314-395)
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 5.5；310 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR measurement conditions pH 5.5；283 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR measurement conditions pH 5.5；295 K；Ionic strength (raw mmCIF value) 0.060；Pressure ambient
NMR sample composition 1mM EGF-AB, 20mM CaCl2 | 95% H2O/5% D2O
NMR sample composition 1mM EGF-AB, 20mM CaCl2 | 99% D2O
NMR sample composition 1mM 15N-EGF-AB, 20mM CaCl2 | 95% H2O/5% D2O
NMR sample composition 1.5mM EGF-A, 20mM CaCl2 | 99% D2O
NMR sample composition 1.5mM EGF-A, 20mM CaCl2 | 95% H2O/5% D2O
Resolution not provided
1IJQ Crystal Structure of the LDL Receptor YWTD-EGF Domain Pair Deposited 2001-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 398–713（316 aa） Fragment：YWTD-E3 DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG4000,2-propanol,HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.250
1IJQ Crystal Structure of the LDL Receptor YWTD-EGF Domain Pair Deposited 2001-04-27 Different construct 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 398–713（316 aa） Fragment：YWTD-E3 DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG4000,2-propanol,HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.250
1LDL THREE-DIMENSIONAL STRUCTURE OF A CYSTEINE-RICH REPEAT FROM THE LOW-DENSITY LIPOPROTEIN RECEPTOR Deposited 1995-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–67（48 aa） Fragment：LIGAND-BINDING DOMAIN, FIRST REPEAT
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1LDR SECOND REPEAT OF THE LDL RECEPTOR LIGAND-BINDING DOMAIN Deposited 1995-08-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 55–104（50 aa） Fragment：LIGAND-BINDING DOMAIN, SECOND REPEAT
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1N7D Extracellular domain of the LDL receptor Deposited 2002-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–720（699 aa） Fragment：extracellular domain, RESIDUES 1-699
Mutation：N494Q, N636Q CA CALCIUM ION × 8 KEG 12-TUNGSTOPHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；298 K；acetate buffer pH 5.3, 1,2-hexanediol, 0.5 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.70 Å R-free 0.382
1XFE Solution structure of the LA7-EGFA pair from the LDL receptor Deposited 2004-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 272–353（82 aa） Fragment：sequence database residues 272-353: includes LDL-receptor class A 7 (residues 274-313), EGF-like 1 (314-353)
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 1:6 molar protein/CaCl2；Pressure ambient
NMR sample composition 0.3 mM LA7-EGFA U-15N,13C 2 mM CaCl2; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.5 mM LA7-EGFA U-15N 10 mM CaCl2; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.6 mMM LA7-EGFA U-15N, 10% 13C 4 mM CaCl2; 99% D2O | 99% D2O
NMR sample composition 1 mM LA7-EGFA 6 mM CaCl2; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2FCW Structure of a Complex Between the Pair of the LDL Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (RAP). Deposited 2005-12-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 107–186（80 aa） Fragment：A Pair of Ligand-Binding Modules 3 and 4
Not recorded NA SODIUM ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；40% MPD, 100 mM HEPES, 75 mM NaCl, 1.25 mM CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.26 Å R-free 0.200
2FCW Structure of a Complex Between the Pair of the LDL Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (RAP). Deposited 2005-12-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 107–186（80 aa） Fragment：A Pair of Ligand-Binding Modules 3 and 4
Not recorded NA SODIUM ION × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 10 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；40% MPD, 100 mM HEPES, 75 mM NaCl, 1.25 mM CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.26 Å R-free 0.200
2KRI Structure of a complex between domain V of beta2-glycoprotein I and the fourth ligand-binding module from LDLR determined with Haddock Deposited 2009-12-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 147–186（40 aa） Fragment：LDL-receptor class A 4 domain
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 25；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_2-1, 100 uM [U-100% 15N] entity_2-2, 300 uM [U-100% 15N] entity_2-3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 600 uM [U-100% 13C; U-100% 15N] entity_1-4, 300 uM [U-100% 15N] entity_1-5, 515 uM [U-100% 15N] entity_1-6, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LGP Solution structure of LA45 from LDLR Deposited 2011-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 144–235（92 aa） Fragment：LDL-receptor class A 4 and A5 domain residues 144-235
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.45；306 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] protein, 5 mM CALCIUM ION, 0.02 % sodium azide, 20 mM [U-99% 2H] HEPES, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] protein, 5 mM CALCIUM ION, 0.02 % sodium azide, 150 mM sodium chloride, 20 mM [U-99% 2H] HEPES, 100% D2O | 100% D2O
Resolution not provided
2M7P RXFP1 utilises hydrophobic moieties on a signalling surface of the LDLa module to mediate receptor activation Deposited 2013-04-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 66–68（3 aa）
Chain A 82–104（23 aa）
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] LDLA-1, 50 mM Immidazole-2, 10 mM CaCl2-3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MG9 Truncated EGF-A Deposited 2013-10-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 314–339（26 aa） Fragment：EGF-A domain, UNP RESIDUES 314-339
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 5.3；283 K；Pressure ambient
NMR sample composition 1 mM egfa-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2W2M WT PCSK9-DELTAC BOUND TO WT EGF-A OF LDLR Deposited 2008-11-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-A DOMAIN, RESIDUES 314-393
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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-A DOMAIN, RESIDUES 314-393
Mutation：YES 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-A DOMAIN, RESIDUES 314-393
Not recorded 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
2W2Q PCSK9-deltaC D374H mutant bound to WT EGF-A of LDLR Deposited 2008-11-03 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-A DOMAIN, RESIDUES 314-393
Not recorded 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
3BPS PCSK9:EGF-A complex Deposited 2007-12-19 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa） Fragment：EGF-like 1, EGF-like 2 domains, UNP residues 314-393
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 mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 aa）
Mutation：H306Y 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 314–393（80 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
3M0C The X-ray Crystal Structure of PCSK9 in Complex with the LDL receptor Deposited 2010-03-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 4–788（785 aa） Fragment：LDLR
Not recorded 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
3SO6 Crystal structure of the LDL receptor tail in complex with autosomal recessive hypercholesterolemia PTB domain Deposited 2011-06-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Q 819–832（14 aa） Fragment：UNP residues 817-832
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES, 30% PEG6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.37 Å R-free 0.206
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 D 314–339（26 aa） Fragment：UNP residues 314-339
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
5OY9 VSV G CR3 Deposited 2017-09-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 108–144（37 aa） Fragment：UNP residues 108-144
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30% PEG 400, 50 mM Tris-HCl pH 8.5, 200 mM CaCl2, 0.2% dodecylmaltoside
Resolution 3.60 Å R-free 0.268
5OYL VSV G CR2 Deposited 2017-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 65–106（42 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2 GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；29% PEG 3000, 100 mM Tris-HCl pH 8.5, 200 mM LiSO4
Resolution 2.25 Å R-free 0.224
9BD8 ApoB 100 beta barrel bound to LDLR beta propeller Deposited 2024-04-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–860（860 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
9BDE Middle Region of Apolipoprotein B 100 bound to Low Density Lipoprotein Receptor Deposited 2024-04-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 1–860（860 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9BDT Apolipoprotein B 100 bound to LDL receptor and legobody Deposited 2024-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 1–860（860 aa）
Chain R 1–860（860 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 66–860（795 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å

33 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LDLR_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 28–107； UniProt 314–393

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

SAXS profile for 2w2p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2w2p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2w2p
Deposition date deposition_date2008-11-03
Structure title titlePCSK9-deltaC D374A mutant bound to WT EGF-A of LDLR
Keywords keywords;HYDROLASE-RECEPTOR COMPLEX, PCSK9, LDLR, PROPROTEIN CONVERTASE, LOW-DENSITY LIPOPROTEIN RECEPTOR, EGF, CARDIOVASCULAR DISEASE, FAMILIAL HYPERCHOLESTEROLEMIA, LIPID METABOLISM, SERINE PROTEASE, HYDROLASE, LIPID TRANSPORT, STEROID METABOLISM, RECEPTOR ;; HYDROLASE/RECEPTOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.68 Å
Radius of gyration Rg (electron density) rg_electron22.83 Å
Forward intensity I(0) i034946000.00
Molecular weight molecular_weight44617.0 kDa
Excluded volume excluded_volume55537 ų
Envelope volume envelope_volume67166 ų
Hydration-shell volume shell_volume24937 ų
Envelope diameter envelope_diameter95.0 Å
Shell Rg shell_rg29.78 Å
Envelope Rg envelope_rg23.59 Å
Shape Rg shape_rg22.81 Å
Total Rg total_rg23.71 Å
Total atoms total_atoms3128
Residues n_residues415
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax89.4 Å
Rg (real space) rg_real23.73 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real3.4950e+07
I(0) uncertainty (real space) i0_real_error5.1320e+05
Rg (reciprocal space) rg_reciprocal23.72 Å
I(0) (reciprocal space) i0_reciprocal34950000.0000
Solution quality estimate total_estimate0.6170
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.9 Å
Skewness Skewness skewness0.470
Kurtosis Kurtosis kurtosis0.007
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7623000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.583; Stabil: 1.000; Sysdev: 0.154; Positv: 1.000; Valcen: 0.830; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2w2pa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.41 — Subtilisin-like
Superfamily Superfamily superfamilyc.41.1 — Subtilisin-like
Family Family familyc.41.1.1 — Subtilases
Domain ID domain_idd2w2pe1
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.11 — EGF/Laminin
Family Family familyg.3.11.0 — automated matches
Domain ID domain_idd2w2pe2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id2w2pA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily200 — Peptidase S8/S53 domain
Domain ID domain_id2w2pE00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
Domain ID domain_id2w2pP01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily80 — Peptidase S8 propeptide/proteinase inhibitor I9
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8. Citations (1)

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9. Files and Curves (10)