Crystal Structure Analysis of Fab1-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Insulin


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
K [auth c]SCOP2B SuperfamilyInsulin-like 8038024 3000307 SCOP2B (2022-06-29)
I [auth a]SCOP2B SuperfamilyInsulin-like 8038024 3000307 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BA [auth P]tRNA_U5-meth_tre5wobP1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
CA [auth R]tRNA_U5-meth_tre5wobR1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
DA [auth T]tRNA_U5-meth_tre5wobT1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
Y [auth J]Acetyltransf_3e5wobJ1 A: beta barrelsX: FAD-linked reductases, C-terminal domain-likeH: FAD-linked reductases-CT: FAD-linked reductases-CF: Acetyltransf_3ECOD (v294.2)
Z [auth L]tRNA_U5-meth_tre5wobL1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
FA [auth X]tRNA_U5-meth_tre5wobX1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
EA [auth V]tRNA_U5-meth_tre5wobV1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
AA [auth N]tRNA_U5-meth_tre5wobN1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
S [auth M]tRNA_U5-meth_tre5wobM1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
T [auth O]tRNA_U5-meth_tre5wobO1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
U [auth Q]tRNA_U5-meth_tre5wobQ1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
W [auth U]tRNA_U5-meth_tre5wobU1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
X [auth W]tRNA_U5-meth_tre5wobW1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
V [auth S]tRNA_U5-meth_tre5wobS1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
R [auth K]tRNA_U5-meth_tre5wobK1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
Q [auth I]Acetyltransf_3e5wobI1 A: beta barrelsX: FAD-linked reductases, C-terminal domain-likeH: FAD-linked reductases-CT: FAD-linked reductases-CF: Acetyltransf_3ECOD (v294.2)
K [auth c]tRNA_U5-meth_tre5wobc1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
O [auth g]tRNA_U5-meth_tre5wobg1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
N [auth f]tRNA_U5-meth_tre5wobf1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
I [auth a]Acetyltransf_3e5woba1 A: beta barrelsX: FAD-linked reductases, C-terminal domain-likeH: FAD-linked reductases-CT: FAD-linked reductases-CF: Acetyltransf_3ECOD (v294.2)
EtRNA_U5-meth_tre5wobE1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
FtRNA_U5-meth_tre5wobF1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
GtRNA_U5-meth_tre5wobG1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
HtRNA_U5-meth_tre5wobH1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
DtRNA_U5-meth_tre5wobD1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
CAcetyltransf_3e5wobC1 A: beta barrelsX: FAD-linked reductases, C-terminal domain-likeH: FAD-linked reductases-CT: FAD-linked reductases-CF: Acetyltransf_3ECOD (v294.2)
BtRNA_U5-meth_tre5wobB1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)
AtRNA_U5-meth_tre5wobA1 A: beta barrelsX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: tRNA_U5-meth_trECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
BA [auth P]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
CA [auth R]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
DA [auth T]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
Y [auth J]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
Z [auth L]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
FA [auth X]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
EA [auth V]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
AA [auth N]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
S [auth M]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
T [auth O]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
U [auth Q]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
W [auth U]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
X [auth W]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
V [auth S]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
R [auth K]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
Q [auth I]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
E3.30.830.10 Alpha Beta 2-Layer Sandwich Cytochrome Bc1 Complex Chain A, domain 1CATH (4.3.0)
F3.30.830.10 Alpha Beta 2-Layer Sandwich Cytochrome Bc1 Complex Chain A, domain 1CATH (4.3.0)
G3.30.830.10 Alpha Beta 2-Layer Sandwich Cytochrome Bc1 Complex Chain A, domain 1CATH (4.3.0)
H3.30.830.10 Alpha Beta 2-Layer Sandwich Cytochrome Bc1 Complex Chain A, domain 1CATH (4.3.0)
D3.30.830.10 Alpha Beta 2-Layer Sandwich Cytochrome Bc1 Complex Chain A, domain 1CATH (4.3.0)
C3.30.830.10 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)
A3.30.830.10 Alpha Beta 2-Layer Sandwich Cytochrome Bc1 Complex Chain A, domain 1CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
Light ChainIGKV1 KappainsulinSAbDab (2026-05-08)
Heavy ChainIGHV3 -insulinSAbDab (2026-05-08)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
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, C, D, E
PF16187Middle or third domain of peptidase_M16 (Peptidase_M16_M)Middle or third domain of peptidase_M16- Family
A, B, C, D, E
PF00675Insulinase (Peptidase family M16) (Peptidase_M16)Insulinase (Peptidase family M16)- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
IDE-bound Fab light chain---
IDE-bound Fab heavy chain---
Insulin
A, B, C, D, E
Insulin-degrading enzyme

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR004825InsulinFamily
IPR022353Insulin, conserved siteConserved Site
IPR036438Insulin-like superfamilyHomologous Superfamily
IPR016179Insulin-likeDomain
IPR022352Insulin/IGF/relaxinFamily
A, B, C, D, E
IPR011249Metalloenzyme, LuxS/M16 peptidase-likeHomologous Superfamily
A, B, C, D, E
IPR001431Peptidase M16, zinc-binding siteBinding Site
A, B, C, D, E
IPR007863Peptidase M16, C-terminalDomain
A, B, C, D, E
IPR054734Coenzyme PQQ synthesis protein F-like, C-terminal lobe, domain 4Domain
A, B, C, D, E
IPR011765Peptidase M16, N-terminalDomain
A, B, C, D, E
IPR050626Peptidase M16Family
A, B, C, D, E
IPR032632Peptidase M16, middle/third domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
P01308
A, B, C, D, E
P14735