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)
I [auth a]SCOP2B SuperfamilyInsulin-like 8038024 3000307 SCOP2B (2022-06-29)
K [auth c]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]e5wobP1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
FA [auth X]e5wobX1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
Y [auth J]e5wobJ1 A: P-loop domains-likeX: Cas7-relatedH: CRISPR-associated protein Cas7f/Csy3T: Acetyltransf_3F:ECOD (20:10:01)
Z [auth L]e5wobL1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
EA [auth V]e5wobV1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
DA [auth T]e5wobT1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
CA [auth R]e5wobR1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
AA [auth N]e5wobN1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
Q [auth I]e5wobI1 A: P-loop domains-likeX: Cas7-relatedH: CRISPR-associated protein Cas7f/Csy3T: Acetyltransf_3F:ECOD (20:10:01)
S [auth M]e5wobM1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
T [auth O]e5wobO1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
U [auth Q]e5wobQ1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
V [auth S]e5wobS1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
W [auth U]e5wobU1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
X [auth W]e5wobW1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
R [auth K]e5wobK1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
I [auth a]e5woba1 A: P-loop domains-likeX: Cas7-relatedH: CRISPR-associated protein Cas7f/Csy3T: Acetyltransf_3F:ECOD (20:10:01)
K [auth c]e5wobc1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
N [auth f]e5wobf1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
O [auth g]e5wobg1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
Ae5wobA1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
Fe5wobF1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
He5wobH1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
Ge5wobG1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
Ee5wobE1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
De5wobD1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)
Ce5wobC1 A: P-loop domains-likeX: Cas7-relatedH: CRISPR-associated protein Cas7f/Csy3T: Acetyltransf_3F:ECOD (20:10:01)
Be5wobB1 A: RING/U-box-likeX: Rubredoxin-relatedH: Rubredoxin-relatedT:F:ECOD (20:10:01)

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)
FA [auth X]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)
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)
AA [auth N]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)
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)
V [auth S]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)
R [auth K]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
A3.30.830.10 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)
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)
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)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
Light ChainIGKV1 KappainsulinSAbDab (2026-03-13)
Heavy ChainIGHV3 -insulinSAbDab (2026-03-13)

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
PharosP01308
A, B, C, D, E
PharosP14735