4XL1 | pdb_00004xl1

Complex of Notch1 (EGF11-13) bound to Delta-like 4 (N-EGF1)

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad4xl1a1 Small proteins Knottins (small inhibitors, toxins, lectins) EGF/Laminin automated matches automated matches Rat (Rattus norvegicus ) [TaxId: 10116 ], SCOPe (2.08)
Ad4xl1a4 Artifacts Tags Tags Tags C-terminal Tags Rat (Rattus norvegicus ) [TaxId: 10116 ], SCOPe (2.08)
C [auth D]d4xl1d1 Small proteins Knottins (small inhibitors, toxins, lectins) EGF/Laminin automated matches automated matches Rat (Rattus norvegicus ) [TaxId: 10116 ], SCOPe (2.08)
C [auth D]d4xl1d5 Artifacts Tags Tags Tags C-terminal Tags Rat (Rattus norvegicus ) [TaxId: 10116 ], SCOPe (2.08)
C [auth D]d4xl1d4 Artifacts Tags Tags Tags N-terminal Tags Rat (Rattus norvegicus ) [TaxId: 10116 ], SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AhEGF_2e4xl1A2 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: hEGF_2ECOD (1.6)
C [auth D]hEGF_2e4xl1D1 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: hEGF_2ECOD (1.6)
BMNNLe4xl1B3 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: C2 domain (From Topology)T: C2 domainF: MNNLECOD (1.6)
BDSLe4xl1B2 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: DSLECOD (1.6)
BEGF_2_like_1e4xl1B1 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: EGF_2_like_1ECOD (1.6)
D [auth E]MNNLe4xl1E2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: C2 domain (From Topology)T: C2 domainF: MNNLECOD (1.6)
D [auth E]DSLe4xl1E3 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: DSLECOD (1.6)
D [auth E]EGF_2_like_1e4xl1E1 A: few secondary structure elementsX: EGF-likeH: EGF-relatedT: EGF/LamininF: EGF_2_like_1ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A2.10.25.10 Mainly Beta Ribbon Laminin LamininCATH (4.3.0)
C [auth D]2.10.25.10 Mainly Beta Ribbon Laminin LamininCATH (4.3.0)
B2.60.40.3510 Mainly Beta Sandwich Immunoglobulin-like CATH (utative)
D [auth E]2.60.40.3510 Mainly Beta Sandwich Immunoglobulin-like CATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A,
C [auth D]		PF00008EGF-like domain (EGF)EGF-like domainThere is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is t ...There is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.
Domain
A,
C [auth D]		PF12661Human growth factor-like EGF (hEGF)Human growth factor-like EGFhEGF, or human growth factor-like EGF, domains have six conserved residues disulfide-bonded into the characteristic 'ababcc' pattern. They are involved in growth and proliferation of cells, in proteins of the Notch/Delta pathway, neurogulin and selec ...hEGF, or human growth factor-like EGF, domains have six conserved residues disulfide-bonded into the characteristic 'ababcc' pattern. They are involved in growth and proliferation of cells, in proteins of the Notch/Delta pathway, neurogulin and selectins. hEGFs are also found in mosaic proteins with four-disulfide laminin EGFs such as aggrecan and perlecan. 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 Cys residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In hEGFs the C-terminal thiol resides in the beta-turn, resulting in shorter loop-lengths between the Cys residues of disulfide 'c', typically C[8-9]XC. These shorter loop-lengths are also typical of the four-disulfide EGF domains, laminin ad integrin. Tandem hEGF domains have six linking residues between terminal cysteines of adjacent domains. hEGF domains may or may not bind calcium in the linker region. hEGF domains with the consensus motif CXD4X[F,Y]XCXC are hydroxylated exclusively in the Asp residue.
Domain
A,
C [auth D]		PF07645Calcium-binding EGF domain (EGF_CA)Calcium-binding EGF domainDomain
B,
D [auth E]		PF01414Delta serrate ligand (DSL)Delta serrate ligandThis family has been redefined to correspond to the EGF-like domain defined by structure. Domain
B,
D [auth E]		PF07657N terminus of Notch ligand C2-like domain (MNNL)N terminus of Notch ligand C2-like domainThis entry represents a region of conserved sequence at the N terminus of several Notch ligand proteins. The entry has been extended to correspond to the C2-like domain defined by the protein structure. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A,
C [auth D]		Neurogenic locus notch homolog protein 1
B,
D [auth E]		Delta-like protein

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A,
C [auth D]		IPR013032EGF-like, conserved siteConserved Site
A,
C [auth D]		IPR022362Neurogenic locus notch homolog protein 1Family
A,
C [auth D]		IPR036770Ankyrin repeat-containing domain superfamilyHomologous Superfamily
A,
C [auth D]		IPR000742EGF-like domainDomain
A,
C [auth D]		IPR035993Notch-like domain superfamilyHomologous Superfamily
A,
C [auth D]		IPR011656Notch, NODP domainDomain
A,
C [auth D]		IPR010660Notch, NOD domainDomain
A,
C [auth D]		IPR008297NotchFamily
A,
C [auth D]		IPR000800Notch domainDomain
A,
C [auth D]		IPR000152EGF-type aspartate/asparagine hydroxylation sitePTM
A,
C [auth D]		IPR001881EGF-like calcium-binding domainDomain
A,
C [auth D]		IPR009030Growth factor receptor cysteine-rich domain superfamilyHomologous Superfamily
A,
C [auth D]		IPR018097EGF-like calcium-binding, conserved siteConserved Site
A,
C [auth D]		IPR002110Ankyrin repeatRepeat
A,
C [auth D]		IPR049883NOTCH1 EGF-like calcium-binding domainDomain
A,
C [auth D]		IPR051022Notch Signaling and Cell Fate DeterminationFamily
A,
C [auth D]		IPR024600Notch, C-terminalDomain
B,
D [auth E]		IPR051830Neurogenic locus notch homologFamily
B,
D [auth E]		IPR001774Delta/Serrate/lag-2 (DSL) proteinDomain
B,
D [auth E]		IPR013032EGF-like, conserved siteConserved Site
B,
D [auth E]		IPR000742EGF-like domainDomain
B,
D [auth E]		IPR011651Notch ligand, N-terminal domainDomain
B,
D [auth E]		IPR009030Growth factor receptor cysteine-rich domain superfamilyHomologous Superfamily
B,
D [auth E]		IPR001881EGF-like calcium-binding domainDomain
B,
D [auth E]		IPR000152EGF-type aspartate/asparagine hydroxylation sitePTM

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
B,
D [auth E]		MLY Parent Component: LYS

RESID:  AA0075

PSI-MOD :  N6,N6-dimethyl-L-lysine MOD:00084