6U38

PCSK9 in complex with a Fab and compound 8

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6u38b1	Alpha and beta proteins (a/b)	Subtilisin-like	Subtilisin-like	Subtilases	Proprotein convertase subtilisin/kexin type 9	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6u38b2	Small proteins	Resistin	Resistin	PCSK9 C-terminal domain-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth L]	d6u38l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth L]	d6u38l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Subtilisin-like	8069727	3000226	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Inhibitor_I9	e6u38A1	A: a+b two layers	X: Alpha-beta plaits	H: Protease propeptides/inhibitors (From Topology)	T: Protease propeptides/inhibitors	F: Inhibitor_I9	ECOD (1.6)
B	PCSK9_C-CRD_2nd	e6u38B4	A: beta duplicates or obligate multimers	X: Resistin (From Topology)	H: Resistin (From Topology)	T: Resistin	F: PCSK9_C-CRD_2nd	ECOD (1.6)
B	PCSK9_C-CRD_1st	e6u38B3	A: beta duplicates or obligate multimers	X: Resistin (From Topology)	H: Resistin (From Topology)	T: Resistin	F: PCSK9_C-CRD_1st	ECOD (1.6)
B	PCSK9_C-CRD_3rd	e6u38B1	A: beta duplicates or obligate multimers	X: Resistin (From Topology)	H: Resistin (From Topology)	T: Resistin	F: PCSK9_C-CRD_3rd	ECOD (1.6)
B	Peptidase_S8	e6u38B2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like (From Topology)	T: Subtilisin-like	F: Peptidase_S8	ECOD (1.6)
C [auth H]	V-set_8	e6u38H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth H]	C1-set_1	e6u38H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D [auth L]	C1-set_4	e6u38L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth L]	V-set	e6u38L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.80	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Peptidase S8 propeptide/proteinase inhibitor I9	CATH (utative)
B	3.40.50.200	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Peptidase S8/S53 domain	CATH (utative)
B	2.60.120.690	Mainly Beta	Sandwich	Jelly Rolls	Proprotein convertase subtilisin/kexin type 9	CATH (utative)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C [auth H]	Antibody Fab Fragment	VH-CH1	Homo sapiens (human)	IGHV3-2301, IGHV3-2302, IGHV3-2303, IGHV3-23D01, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG111	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
D [auth L]	Antibody Fab Fragment	L-KAPPA	Homo sapiens (human)	IGKV3D-1101, IGKV3D-1102, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H]	Heavy Chain	IGHV3	-	proprotein convertase subtilisin/kexin type 9	SAbDab (2024-04-19)
D [auth L]	Light Chain	IGKV3	Kappa	proprotein convertase subtilisin/kexin type 9	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18463	Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain (PCSK9_C3)	Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain	This entry represents a subdomain found in the C-terminal cysteine/histidine-rich domain (CRD) of PCSK9 (also known as neural apoptosis-regulated convertase, NARC-1) [1]. PCSK9 has been shown to regulate circulating LDL-R levels by controlling LDL-R ...	This entry represents a subdomain found in the C-terminal cysteine/histidine-rich domain (CRD) of PCSK9 (also known as neural apoptosis-regulated convertase, NARC-1) [1]. PCSK9 has been shown to regulate circulating LDL-R levels by controlling LDL-R degradation. Furthermore, numerous mutations in the PCSK9 gene have been identified and associated with hypercholesterolemia (gain of function) or hypocholesterolemia (loss of function) [2]. The fully folded CRD, shows structural similarity to the resistin homotrimer, a small cytokine associated with obesity and diabetes. The C-terminal domain from PCSK9 consists of three, three-stranded beta-subdomains arranged in a pseudothreefold, and each of the subdomains in the CRD of PCSK9 consists of three structurally conserved disulfide bonds [1].	Domain
A, B	PF18464	Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain (PCSK9_C2)	Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain	This entry represents a subdomain found in the C-terminal cysteine/histidine-rich domain (CRD) of PCSK9 (also known as neural apoptosis-regulated convertase, NARC-1) [1]. PCSK9 has been shown to regulate circulating LDL-R levels by controlling LDL-R ...	This entry represents a subdomain found in the C-terminal cysteine/histidine-rich domain (CRD) of PCSK9 (also known as neural apoptosis-regulated convertase, NARC-1) [1]. PCSK9 has been shown to regulate circulating LDL-R levels by controlling LDL-R degradation. Furthermore, numerous mutations in the PCSK9 gene have been identified and associated with hypercholesterolemia (gain of function) or hypocholesterolemia (loss of function) [2]. The fully folded CRD, shows structural similarity to the resistin homotrimer, a small cytokine associated with obesity and diabetes. The C-terminal domain from PCSK9 consists of three, three-stranded beta-subdomains arranged in a pseudothreefold, and each of the subdomains in the CRD of PCSK9 consists of three structurally conserved disulfide bonds [1].	Domain
A, B	PF05922	Peptidase inhibitor I9 (Inhibitor_I9)	Peptidase inhibitor I9	This family includes the proteinase B inhibitor from Saccharomyces cerevisiae and the activation peptides from peptidases of the subtilisin family. The subtilisin propeptides are known to function as molecular chaperones, assisting in the folding of ...	This family includes the proteinase B inhibitor from Saccharomyces cerevisiae and the activation peptides from peptidases of the subtilisin family. The subtilisin propeptides are known to function as molecular chaperones, assisting in the folding of the mature peptidase [1], but have also been shown to act as 'temporary inhibitors' [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Proprotein convertase subtilisin/kexin type 9	molecular function inhibitor activity sodium channel inhibitor activity channel regulator activity transporter inhibitor activity ion channel regulator activity ion channel inhibitor activity molecular function regulator activity sodium channel regulator activity transporter regulator activity channel inhibitor activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity molecular function inhibitor activity sodium channel inhibitor activity channel regulator activity transporter inhibitor activity ion channel regulator activity ion channel inhibitor activity molecular function regulator activity sodium channel regulator activity transporter regulator activity channel inhibitor activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity lipoprotein particle binding protein-containing complex binding protein binding binding protein-lipid complex binding very-low-density lipoprotein particle binding apolipoprotein binding signaling receptor binding apolipoprotein receptor binding RNA binding organic cyclic compound binding nucleic acid binding low-density lipoprotein particle binding signaling receptor inhibitor activity signaling receptor regulator activity low-density lipoprotein particle receptor binding lipoprotein particle receptor binding very-low-density lipoprotein particle receptor binding	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein autoprocessing biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein autoprocessing biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process apoptotic process cell death programmed cell death regulation of biological process neuron apoptotic process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of neuron apoptotic process positive regulation of cellular process regulation of neuron apoptotic process regulation of binding negative regulation of binding negative regulation of molecular function regulation of low-density lipoprotein particle receptor binding regulation of protein binding negative regulation of receptor binding regulation of molecular function regulation of receptor binding negative regulation of protein binding negative regulation of low-density lipoprotein particle receptor binding regulation of localization import into cell regulation of cellular component organization receptor internalization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis regulation of receptor internalization vesicle-mediated transport cellular component organization localization negative regulation of cellular process cellular component organization or biogenesis regulation of endocytosis negative regulation of cellular component organization regulation of transport negative regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization endocytosis receptor-mediated endocytosis negative regulation of receptor internalization receptor catabolic process catabolic process positive regulation of protein metabolic process positive regulation of cellular metabolic process macromolecule catabolic process regulation of primary metabolic process cellular catabolic process positive regulation of metabolic process receptor metabolic process positive regulation of macromolecule metabolic process regulation of low-density lipoprotein particle receptor catabolic process positive regulation of receptor catabolic process organonitrogen compound catabolic process regulation of protein metabolic process low-density lipoprotein particle receptor catabolic process regulation of cellular metabolic process protein catabolic process regulation of macromolecule metabolic process regulation of catabolic process positive regulation of low-density lipoprotein particle receptor catabolic process positive regulation of protein catabolic process positive regulation of catabolic process low-density lipoprotein receptor particle metabolic process regulation of receptor catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process organic substance catabolic process regulation of metabolic process regulation of protein catabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to starvation multicellular organismal process regulation of plasma lipoprotein particle levels regulation of low-density lipoprotein particle clearance negative regulation of low-density lipoprotein particle clearance plasma lipoprotein particle clearance negative regulation of lipoprotein particle clearance regulation of lipoprotein particle clearance regulation of multicellular organismal process low-density lipoprotein particle clearance negative regulation of multicellular organismal process negative regulation of low-density lipoprotein receptor activity negative regulation of ion transmembrane transporter activity monoatomic ion transmembrane transport negative regulation of monoatomic ion transport regulation of transmembrane transporter activity sodium ion transmembrane transport regulation of monoatomic ion transmembrane transport regulation of sodium ion transport negative regulation of sodium ion transmembrane transporter activity regulation of sodium ion transmembrane transport metal ion transport negative regulation of transmembrane transport regulation of transporter activity monoatomic cation transmembrane transport regulation of sodium ion transmembrane transporter activity negative regulation of monoatomic ion transmembrane transport monoatomic ion transport negative regulation of cation transmembrane transport monoatomic cation transport regulation of metal ion transport regulation of monoatomic ion transmembrane transporter activity regulation of monoatomic ion transport negative regulation of transporter activity negative regulation of sodium ion transmembrane transport inorganic ion transmembrane transport inorganic cation transmembrane transport transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport negative regulation of sodium ion transport sodium ion transport regulation of signaling signaling regulation of signaling receptor activity regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication signal transduction negative regulation of sterol transport regulation of receptor-mediated endocytosis involved in cholesterol transport negative regulation of lipid localization regulation of intracellular cholesterol transport establishment of localization in cell sterol transport negative regulation of intracellular lipid transport regulation of intracellular transport regulation of sterol transport intracellular lipid transport organic substance transport intracellular transport lipid transport negative regulation of intracellular sterol transport cholesterol transport cellular localization regulation of intracellular sterol transport negative regulation of intracellular cholesterol transport intracellular cholesterol transport regulation of lipid transport organic hydroxy compound transport intracellular sterol transport negative regulation of receptor-mediated endocytosis involved in cholesterol transport receptor-mediated endocytosis involved in cholesterol transport regulation of cholesterol transport negative regulation of intracellular transport negative regulation of lipid transport regulation of intracellular lipid transport lipid localization negative regulation of cholesterol transport regulation of lipid localization regulation of cellular localization macromolecule localization developmental process multicellular organism development anatomical structure development animal organ development kidney development renal system development system development hepaticobiliary system development gland development liver development neurogenesis cellular developmental process cell differentiation nervous system development phospholipid metabolic process organophosphate metabolic process cellular lipid metabolic process phosphate-containing compound metabolic process phosphorus metabolic process lipid metabolic process positive regulation of cellular component organization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis positive regulation of receptor internalization positive regulation of transport sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis generation of neurons neuron differentiation organic hydroxy compound metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process organic cyclic compound metabolic process secondary alcohol metabolic process small molecule metabolic process vacuolar transport lysosomal transport lipoprotein metabolic process negative regulation of signaling regulation of receptor recycling negative regulation of receptor recycling negative regulation of metabolic process receptor recycling negative regulation of macromolecule metabolic process neutral lipid metabolic process triglyceride metabolic process glycerolipid metabolic process acylglycerol metabolic process cellular response to nitrogen compound response to organic substance response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to organonitrogen compound response to hormone response to chemical response to insulin cellular response to organic substance cellular response to insulin stimulus cellular response to hormone stimulus	membrane-bounded organelle intracellular anatomical structure intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle COPII-coated ER to Golgi transport vesicle cytoplasmic vesicle organelle coated vesicle cytoplasm vesicle PCSK9-AnxA2 complex protein-containing complex membrane-bounded organelle intracellular anatomical structure intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle COPII-coated ER to Golgi transport vesicle cytoplasmic vesicle organelle coated vesicle cytoplasm vesicle PCSK9-AnxA2 complex protein-containing complex vacuolar membrane membrane lytic vacuole vacuole lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane lysosome Golgi apparatus endomembrane system membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum perinuclear region of cytoplasm extracellular region extracellular space endosome membrane endolysosome membrane endolysosome vesicle membrane endosome cytoplasmic vesicle membrane cell surface cell periphery plasma membrane early endosome PCSK9-LDLR complex extrinsic component of plasma membrane extrinsic component of external side of plasma membrane extrinsic component of membrane external side of plasma membrane side of membrane late endosome
C [auth H]	Fab Heavy Chain	-	-	-
D [auth L]	Fab Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR041052	Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2	Domain
A, B	IPR037045	Peptidase S8 propeptide/proteinase inhibitor I9 superfamily	Homologous Superfamily
A, B	IPR010259	Peptidase S8 propeptide/proteinase inhibitor I9	Domain
A, B	IPR000209	Peptidase S8/S53 domain	Domain
A, B	IPR015500	Peptidase S8, subtilisin-related	Family
A, B	IPR041051	Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3	Domain
A, B	IPR034193	Proteinase K-like catalytic domain	Domain
A, B	IPR041254	Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1	Domain
A, B	IPR036852	Peptidase S8/S53 domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8NBP7	Hypercholesterolemia coronary artery disease hypercholesterolemia, autosomal dominant, 3 atherosclerosis abetalipoproteinemia familial hypercholesterolemia kidney Wilms tumor inborn errors of metabolism large cell medulloblastoma myocardial infarction pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis abdominal aortic aneurysm hypolipoproteinemia inherited lipid metabolism disorder Hypercholesterolemia coronary artery disease hypercholesterolemia, autosomal dominant, 3 atherosclerosis abetalipoproteinemia familial hypercholesterolemia kidney Wilms tumor inborn errors of metabolism large cell medulloblastoma myocardial infarction pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis abdominal aortic aneurysm hypolipoproteinemia inherited lipid metabolism disorder non-small cell lung carcinoma Perlman syndrome cardiovascular disease heart disease inborn carbohydrate metabolic disorder lung adenocarcinoma pancreatic ductal adenocarcinoma psoriasis arteriosclerosis disorder Crohn disease hereditary Wilms tumor hypercholesterolemia, familial, 1

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.