6B70

Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy chain, FAB H11-E light chain and insulin


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APeptidase_M16_M_Ce6b70A2 A: a+b two layersX: LuxS, MPP, ThrRS/AlaRS common domainH: LuxS, MPP, ThrRS/AlaRS common domainT: LuxS/MPP-like metallohydrolaseF: Peptidase_M16_M_CECOD (1.6)
APeptidase_M16_M_Ne6b70A4 A: a+b two layersX: LuxS, MPP, ThrRS/AlaRS common domainH: LuxS, MPP, ThrRS/AlaRS common domainT: LuxS/MPP-like metallohydrolaseF: Peptidase_M16_M_NECOD (1.6)
APeptidase_M16_C_2e6b70A3 A: a+b two layersX: LuxS, MPP, ThrRS/AlaRS common domainH: LuxS, MPP, ThrRS/AlaRS common domainT: LuxS/MPP-like metallohydrolaseF: Peptidase_M16_C_2ECOD (1.6)
APeptidase_M16e6b70A1 A: a+b two layersX: LuxS, MPP, ThrRS/AlaRS common domainH: LuxS, MPP, ThrRS/AlaRS common domainT: LuxS/MPP-like metallohydrolaseF: Peptidase_M16ECOD (1.6)
BPeptidase_M16_M_Ce6b70B4 A: a+b two layersX: LuxS, MPP, ThrRS/AlaRS common domainH: LuxS, MPP, ThrRS/AlaRS common domainT: LuxS/MPP-like metallohydrolaseF: Peptidase_M16_M_CECOD (1.6)
BPeptidase_M16_M_Ne6b70B2 A: a+b two layersX: LuxS, MPP, ThrRS/AlaRS common domainH: LuxS, MPP, ThrRS/AlaRS common domainT: LuxS/MPP-like metallohydrolaseF: Peptidase_M16_M_NECOD (1.6)
BPeptidase_M16_C_2e6b70B1 A: a+b two layersX: LuxS, MPP, ThrRS/AlaRS common domainH: LuxS, MPP, ThrRS/AlaRS common domainT: LuxS/MPP-like metallohydrolaseF: Peptidase_M16_C_2ECOD (1.6)
BPeptidase_M16e6b70B3 A: a+b two layersX: LuxS, MPP, ThrRS/AlaRS common domainH: LuxS, MPP, ThrRS/AlaRS common domainT: LuxS/MPP-like metallohydrolaseF: Peptidase_M16ECOD (1.6)
CV-set_8e6b70C2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
CC1-set_1e6b70C1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_1ECOD (1.6)
EV-set_8e6b70E1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
EC1-set_1e6b70E2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_1ECOD (1.6)
G [auth a]Insuline6b70a1 A: few secondary structure elementsX: Insulin-like (From Topology)H: Insulin-like (From Topology)T: Insulin-likeF: InsulinECOD (1.6)
DC1-set_4e6b70D2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_4ECOD (1.6)
DV-sete6b70D1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
FC1-set_4e6b70F2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_4ECOD (1.6)
FV-sete6b70F1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.30.830.10 Alpha Beta 2-Layer Sandwich Cytochrome Bc1 Complex Chain A, domain 1CATH (4.3.0)
B3.30.830.10 Alpha Beta 2-Layer Sandwich Cytochrome Bc1 Complex Chain A, domain 1CATH (4.3.0)
C2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
E2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
D2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
F2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
C, E
Fab H11-E VH-CH1 Homo sapiens (human) IGHV3-66*01, IGHV3-66*02, IGHV3-66*04, IGHJ4*01, IGHJ4*02, IGHJ4*03, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_KAPPA IMGT (202449-0)
D, F
Fab H11-E L-KAPPA Homo sapiens (human) IGKV1-39*01, IGKV1D-39*01, IGKJ1*01, IGKC*01 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-1_KAPPA IMGT (202449-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
C, E
Heavy ChainIGHV3 -insulin, insulin-degrading enzymeSAbDab (2024-12-13)
D, F
Light ChainIGKV1 Kappainsulin, insulin-degrading enzymeSAbDab (2024-12-13)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF05193Peptidase M16 inactive domain (Peptidase_M16_C)Peptidase M16 inactive domainPeptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp [1].Domain
A, B
PF16187Middle or third domain of peptidase_M16 (Peptidase_M16_M)Middle or third domain of peptidase_M16- Family
A, B
PF00675Insulinase (Peptidase family M16) (Peptidase_M16)Insulinase (Peptidase family M16)- Family
C, E
PF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.Domain
C, E
PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain
D, F
PF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.Domain
D, F
PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
Insulin-degrading enzyme
C, E
FAB H11-E heavy chain-
G [auth a],
H [auth c]
Insulin
D, F
FAB H11-E light chain- -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B
IPR011249Metalloenzyme, LuxS/M16 peptidase-likeHomologous Superfamily
A, B
IPR050626Peptidase M16Family
A, B
IPR032632Peptidase M16, middle/third domainDomain
A, B
IPR001431Peptidase M16, zinc-binding siteBinding Site
A, B
IPR007863Peptidase M16, C-terminalDomain
A, B
IPR054734Coenzyme PQQ synthesis protein F-like, C-terminal lobe, domain 4Domain
A, B
IPR011765Peptidase M16, N-terminalDomain
C, E
IPR003597Immunoglobulin C1-setDomain
C, E
IPR013783Immunoglobulin-like foldHomologous Superfamily
C, E
IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
C, E
IPR013106Immunoglobulin V-set domainDomain
C, E
IPR003599Immunoglobulin domain subtypeDomain
C, E
IPR007110Immunoglobulin-like domainDomain
C, E
IPR050380Immune Recognition and Response ModulatorsFamily
C, E
IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
G [auth a],
H [auth c]
IPR004825InsulinFamily
G [auth a],
H [auth c]
IPR022353Insulin, conserved siteConserved Site
G [auth a],
H [auth c]
IPR036438Insulin-like superfamilyHomologous Superfamily
G [auth a],
H [auth c]
IPR022352Insulin familyFamily
G [auth a],
H [auth c]
IPR016179Insulin-likeDomain
D, F
IPR003597Immunoglobulin C1-setDomain
D, F
IPR050150Immunoglobulin Variable Light ChainFamily
D, F
IPR013783Immunoglobulin-like foldHomologous Superfamily
D, F
IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
D, F
IPR013106Immunoglobulin V-set domainDomain
D, F
IPR003599Immunoglobulin domain subtypeDomain
D, F
IPR007110Immunoglobulin-like domainDomain
D, F
IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A, B
PharosP14735
G [auth a],
H [auth c]
PharosP01308