3P5B | pdb_00003p5b

The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
B [auth A]SCOP2B SuperfamilySubtilisin-like 8069727 3000226 SCOP2B (2022-06-29)
C [auth L]SCOP2B SuperfamilyEGF/Laminin-like 8034030 3000412 SCOP2B (2022-06-29)
C [auth L]SCOP2B SuperfamilyYWTD domain-like 8034029 3000494 SCOP2B (2022-06-29)
C [auth L]SCOP2B SuperfamilyEGF/Laminin-like 8056609 3000412 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth P]Inhibitor_I9e3p5bP2 A: a+b two layersX: Alpha-beta plaitsH: Protease propeptides/inhibitors (From Topology)T: Protease propeptides/inhibitorsF: Inhibitor_I9ECOD (1.6)
B [auth A]PCSK9_C-CRD_2nde3p5bA4 A: beta duplicates or obligate multimersX: Resistin (From Topology)H: Resistin (From Topology)T: ResistinF: PCSK9_C-CRD_2ndECOD (1.6)
B [auth A]PCSK9_C-CRD_1ste3p5bA2 A: beta duplicates or obligate multimersX: Resistin (From Topology)H: Resistin (From Topology)T: ResistinF: PCSK9_C-CRD_1stECOD (1.6)
B [auth A]PCSK9_C-CRD_3rde3p5bA5 A: beta duplicates or obligate multimersX: Resistin (From Topology)H: Resistin (From Topology)T: ResistinF: PCSK9_C-CRD_3rdECOD (1.6)
B [auth A]Peptidase_S8e3p5bA1 A: a/b three-layered sandwichesX: Subtilisin-likeH: Subtilisin-like (From Topology)T: Subtilisin-likeF: Peptidase_S8ECOD (1.6)
C [auth L]SGL_5e3p5bL1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 6-bladedF: SGL_5ECOD (1.6)
C [auth L]FXa_inhibitione3p5bL4 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: FXa_inhibitionECOD (1.6)
C [auth L]EGF_CAe3p5bL5 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: EGF_CAECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth P]PF05922Peptidase inhibitor I9 (Inhibitor_I9)Peptidase inhibitor I9This 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 ...Domain
B [auth A]PF18463Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain (PCSK9_C3)Proprotein convertase subtilisin-like/kexin type 9 C-terminal domainThis 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 ...Domain
B [auth A]PF18464Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain (PCSK9_C2)Proprotein convertase subtilisin-like/kexin type 9 C-terminal domainThis 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 ...Domain
B [auth A]PF18459Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain (PCSK9_C1)Proprotein convertase subtilisin-like/kexin type 9 C-terminal domainThis 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 ...Domain
C [auth L]PF14670Coagulation Factor Xa inhibitory site (FXa_inhibition)Coagulation Factor Xa inhibitory siteThis short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442 [1]. Domain
C [auth L]PF00058Low-density lipoprotein receptor repeat class B (Ldl_recept_b)Low-density lipoprotein receptor repeat class B- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth P]Proprotein convertase subtilisin/kexin type 9
B [auth A]Proprotein convertase subtilisin/kexin type 9
C [auth L]Low density lipoprotein receptor variant

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth P]IPR041052Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2Domain
A [auth P]IPR037045Peptidase S8 propeptide/proteinase inhibitor I9 superfamilyHomologous Superfamily
A [auth P]IPR010259Peptidase S8 propeptide/proteinase inhibitor I9Domain
A [auth P]IPR000209Peptidase S8/S53 domainDomain
A [auth P]IPR015500Peptidase S8, subtilisin-relatedFamily
A [auth P]IPR041051Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3Domain
A [auth P]IPR050131Subtilisin-like serine proteaseFamily
A [auth P]IPR034193Proteinase K-like catalytic domainDomain
A [auth P]IPR041254Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1Domain
A [auth P]IPR036852Peptidase S8/S53 domain superfamilyHomologous Superfamily
B [auth A]IPR041052Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2Domain
B [auth A]IPR037045Peptidase S8 propeptide/proteinase inhibitor I9 superfamilyHomologous Superfamily
B [auth A]IPR010259Peptidase S8 propeptide/proteinase inhibitor I9Domain
B [auth A]IPR000209Peptidase S8/S53 domainDomain
B [auth A]IPR015500Peptidase S8, subtilisin-relatedFamily
B [auth A]IPR041051Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3Domain
B [auth A]IPR050131Subtilisin-like serine proteaseFamily
B [auth A]IPR034193Proteinase K-like catalytic domainDomain
B [auth A]IPR041254Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1Domain
B [auth A]IPR036852Peptidase S8/S53 domain superfamilyHomologous Superfamily
C [auth L]IPR018097EGF-like calcium-binding, conserved siteConserved Site
C [auth L]IPR036055LDL receptor-like superfamilyHomologous Superfamily
C [auth L]IPR049883NOTCH1 EGF-like calcium-binding domainDomain
C [auth L]IPR000033LDLR class B repeatRepeat
C [auth L]IPR001881EGF-like calcium-binding domainDomain
C [auth L]IPR023415Low-density lipoprotein (LDL) receptor class A, conserved siteConserved Site
C [auth L]IPR011042Six-bladed beta-propeller, TolB-likeHomologous Superfamily
C [auth L]IPR002172Low-density lipoprotein (LDL) receptor class A repeatRepeat
C [auth L]IPR000742EGF-like domainDomain
C [auth L]IPR051221Low-density lipoprotein receptor-relatedFamily
C [auth L]IPR009030Growth factor receptor cysteine-rich domain superfamilyHomologous Superfamily
C [auth L]IPR000152EGF-type aspartate/asparagine hydroxylation sitePTM

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A [auth P]PharosQ8NBP7
B [auth A]PharosQ8NBP7
C [auth L]PharosP01130