3V65 | pdb_00003v65

Crystal structure of agrin and LRP4 complex

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyConcanavalin A-like lectins/glucanases 8079972 3000120 SCOP2B (2022-06-29)
D [auth C]SCOP2B SuperfamilyConcanavalin A-like lectins/glucanases 8079972 3000120 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Be3v65B1 A: a/b three-layered sandwichesX: Thioredoxin-likeH: Thioredoxin-likeT: Thioredoxin-likeF:ECOD (v294.1)
BSigma70_r2,Sigma70_nere3v65B2 A: a/b three-layered sandwichesX: Lipocalins/StreptavidinH: SAM/DNA-glycosylaseT: SAM domain-likeF: Sigma70_r2,Sigma70_nerECOD (v294.1)
C [auth D]LRR_adjacente3v65D2 A: a/b three-layered sandwichesX: Lipocalins/StreptavidinH: Fibronectin type I module-likeT: Fibronectin type I moduleF: LRR_adjacentECOD (v294.1)
C [auth D]tRNA-synt_1_2e3v65D5 A: a/b three-layered sandwichesX: Lipocalins/StreptavidinH: RIFT-relatedT: acid proteaseF: tRNA-synt_1_2ECOD (v294.1)
ASmpA_OmlAe3v65A1 A: a/b three-layered sandwichesX: beta-GraspH: HTHT: winged helix domainF: SmpA_OmlAECOD (v294.1)
D [auth C]SmpA_OmlAe3v65C1 A: a/b three-layered sandwichesX: beta-GraspH: HTHT: winged helix domainF: SmpA_OmlAECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
B2.10.25.10 Mainly Beta Ribbon Laminin LamininCATH (4.3.0)
B2.120.10.30 Mainly Beta 6 Propeller Neuraminidase TolB, C-terminal domainCATH (4.3.0)
C [auth D]2.10.25.10 Mainly Beta Ribbon Laminin LamininCATH (4.3.0)
C [auth D]2.120.10.30 Mainly Beta 6 Propeller Neuraminidase TolB, C-terminal domainCATH (4.3.0)
A2.60.120.200 Mainly Beta Sandwich Jelly Rolls CATH (4.3.0)
D [auth C]2.60.120.200 Mainly Beta Sandwich Jelly Rolls CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B,
C [auth D]		PF12662Complement Clr-like EGF-like (cEGF)Complement Clr-like EGF-likecEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL recepto ...cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue.
Domain
B,
C [auth D]		PF00058Low-density lipoprotein receptor repeat class B (Ldl_recept_b)Low-density lipoprotein receptor repeat class B- Repeat
A,
D [auth C]		PF00054Laminin G domain (Laminin_G_1)Laminin G domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B,
C [auth D]		Low-density lipoprotein receptor-related protein 4
A,
D [auth C]		Agrin

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
B,
C [auth D]		IPR018097EGF-like calcium-binding, conserved siteConserved Site
B,
C [auth D]		IPR026823Complement Clr-like EGF domainDomain
B,
C [auth D]		IPR036055LDL receptor-like superfamilyHomologous Superfamily
B,
C [auth D]		IPR000033LDLR class B repeatRepeat
B,
C [auth D]		IPR001881EGF-like calcium-binding domainDomain
B,
C [auth D]		IPR023415Low-density lipoprotein (LDL) receptor class A, conserved siteConserved Site
B,
C [auth D]		IPR011042Six-bladed beta-propeller, TolB-likeHomologous Superfamily
B,
C [auth D]		IPR002172Low-density lipoprotein (LDL) receptor class A repeatRepeat
B,
C [auth D]		IPR000742EGF-like domainDomain
B,
C [auth D]		IPR051221Low-density lipoprotein receptor-relatedFamily
B,
C [auth D]		IPR009030Growth factor receptor cysteine-rich domain superfamilyHomologous Superfamily
A,
D [auth C]		IPR050372Neurexin-related cell adhesion and synaptic proteinFamily
A,
D [auth C]		IPR013320Concanavalin A-like lectin/glucanase domain superfamilyHomologous Superfamily
A,
D [auth C]		IPR002049Laminin-type EGF domainDomain
A,
D [auth C]		IPR003884Factor I / membrane attack complexDomain
A,
D [auth C]		IPR003645Follistatin-like, N-terminalDomain
A,
D [auth C]		IPR001881EGF-like calcium-binding domainDomain
A,
D [auth C]		IPR036364SEA domain superfamilyHomologous Superfamily
A,
D [auth C]		IPR000082SEA domainDomain
A,
D [auth C]		IPR036058Kazal domain superfamilyHomologous Superfamily
A,
D [auth C]		IPR002350Kazal domainDomain
A,
D [auth C]		IPR000742EGF-like domainDomain
A,
D [auth C]		IPR001791Laminin G domainDomain