5WOB | pdb_00005wob

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)
O [auth g]Rase5wobg1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
N [auth f]Rase5wobf1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
K [auth c]Rase5wobc1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
I [auth a]Acetyltransf_3e5woba1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: Acetyltransf_3ECOD (develop294)
Z [auth L]Rase5wobL1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
Y [auth J]Acetyltransf_3e5wobJ1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: Acetyltransf_3ECOD (develop294)
FA [auth X]Rase5wobX1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
EA [auth V]Rase5wobV1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
DA [auth T]Rase5wobT1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
CA [auth R]Rase5wobR1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
BA [auth P]Rase5wobP1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
AA [auth N]Rase5wobN1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
X [auth W]Rase5wobW1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
W [auth U]Rase5wobU1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
V [auth S]Rase5wobS1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
U [auth Q]Rase5wobQ1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
T [auth O]Rase5wobO1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
S [auth M]Rase5wobM1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
R [auth K]Rase5wobK1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
Q [auth I]Acetyltransf_3e5wobI1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: Acetyltransf_3ECOD (develop294)
HRase5wobH1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
GRase5wobG1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
FRase5wobF1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
ERase5wobE1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
DRase5wobD1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
CAcetyltransf_3e5wobC1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: Acetyltransf_3ECOD (develop294)
BRase5wobB1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)
ARase5wobA1 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Rubredoxin-relatedF: RasECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
Z [auth L]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)
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)
DA [auth T]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)
BA [auth P]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)
X [auth W]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)
V [auth S]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)
T [auth O]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)
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)
H3.30.830.10 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)
F3.30.830.10 Alpha Beta 2-Layer Sandwich Cytochrome Bc1 Complex Chain A, domain 1CATH (4.3.0)
E3.30.830.10 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 (2026-03-20)
Heavy ChainIGHV3 -insulinSAbDab (2026-03-20)

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
Insulin
IDE-bound Fab light chain---
IDE-bound Fab heavy chain---
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
PharosP01308
A, B, C, D, E
PharosP14735