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3OFI

Crystal structure of human insulin-degrading enzyme in complex with ubiquitin

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0001618molecular_functionvirus receptor activity
A0003824molecular_functioncatalytic activity
A0004175molecular_functionendopeptidase activity
A0004222molecular_functionmetalloendopeptidase activity
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005576cellular_componentextracellular region
A0005615cellular_componentextracellular space
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005777cellular_componentperoxisome
A0005782cellular_componentperoxisomal matrix
A0005829cellular_componentcytosol
A0005886cellular_componentplasma membrane
A0006508biological_processproteolysis
A0008152biological_processmetabolic process
A0008233molecular_functionpeptidase activity
A0008237molecular_functionmetallopeptidase activity
A0008270molecular_functionzinc ion binding
A0008286biological_processinsulin receptor signaling pathway
A0009897cellular_componentexternal side of plasma membrane
A0009986cellular_componentcell surface
A0010815biological_processbradykinin catabolic process
A0010992biological_processubiquitin recycling
A0016020cellular_componentmembrane
A0016323cellular_componentbasolateral plasma membrane
A0016787molecular_functionhydrolase activity
A0019885biological_processantigen processing and presentation of endogenous peptide antigen via MHC class I
A0030163biological_processprotein catabolic process
A0032092biological_processpositive regulation of protein binding
A0042277molecular_functionpeptide binding
A0042447biological_processhormone catabolic process
A0042803molecular_functionprotein homodimerization activity
A0043171biological_processpeptide catabolic process
A0043559molecular_functioninsulin binding
A0045732biological_processpositive regulation of protein catabolic process
A0046718biological_processsymbiont entry into host cell
A0046872molecular_functionmetal ion binding
A0050435biological_processamyloid-beta metabolic process
A0051603biological_processproteolysis involved in protein catabolic process
A0070062cellular_componentextracellular exosome
A0097242biological_processamyloid-beta clearance
A0140036molecular_functionubiquitin-modified protein reader activity
A0150094biological_processamyloid-beta clearance by cellular catabolic process
A1901142biological_processinsulin metabolic process
A1901143biological_processinsulin catabolic process
A1903715biological_processregulation of aerobic respiration
B0000166molecular_functionnucleotide binding
B0001618molecular_functionvirus receptor activity
B0003824molecular_functioncatalytic activity
B0004175molecular_functionendopeptidase activity
B0004222molecular_functionmetalloendopeptidase activity
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005576cellular_componentextracellular region
B0005615cellular_componentextracellular space
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005777cellular_componentperoxisome
B0005782cellular_componentperoxisomal matrix
B0005829cellular_componentcytosol
B0005886cellular_componentplasma membrane
B0006508biological_processproteolysis
B0008152biological_processmetabolic process
B0008233molecular_functionpeptidase activity
B0008237molecular_functionmetallopeptidase activity
B0008270molecular_functionzinc ion binding
B0008286biological_processinsulin receptor signaling pathway
B0009897cellular_componentexternal side of plasma membrane
B0009986cellular_componentcell surface
B0010815biological_processbradykinin catabolic process
B0010992biological_processubiquitin recycling
B0016020cellular_componentmembrane
B0016323cellular_componentbasolateral plasma membrane
B0016787molecular_functionhydrolase activity
B0019885biological_processantigen processing and presentation of endogenous peptide antigen via MHC class I
B0030163biological_processprotein catabolic process
B0032092biological_processpositive regulation of protein binding
B0042277molecular_functionpeptide binding
B0042447biological_processhormone catabolic process
B0042803molecular_functionprotein homodimerization activity
B0043171biological_processpeptide catabolic process
B0043559molecular_functioninsulin binding
B0045732biological_processpositive regulation of protein catabolic process
B0046718biological_processsymbiont entry into host cell
B0046872molecular_functionmetal ion binding
B0050435biological_processamyloid-beta metabolic process
B0051603biological_processproteolysis involved in protein catabolic process
B0070062cellular_componentextracellular exosome
B0097242biological_processamyloid-beta clearance
B0140036molecular_functionubiquitin-modified protein reader activity
B0150094biological_processamyloid-beta clearance by cellular catabolic process
B1901142biological_processinsulin metabolic process
B1901143biological_processinsulin catabolic process
B1903715biological_processregulation of aerobic respiration
Functional Information from PDB Data
site_idAC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ZN A 2012
ChainResidue
AHIS108
AHIS112
AGLU189

site_idAC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE DIO A 2013
ChainResidue
AHOH3213
AHOH3228
AGLN800
AALA840
AASN841
AGLY842
ASER913
AGLN915

site_idAC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ZN B 2012
ChainResidue
BHIS108
BHIS112
BGLU189

site_idAC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE DIO B 2013
ChainResidue
BGLU205
BARG477
BALA479

site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE DIO B 2014
ChainResidue
BGLN800
BALA840
BASN841
BGLY842

Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
CLYS27-ASP52

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsSITE: Interacts with activating enzyme
ChainResidueDetails
CARG54
CARG72
DARG54
DARG72

site_idSWS_FT_FI2
Number of Residues2
DetailsSITE: Essential for function
ChainResidueDetails
CHIS68
DHIS68
AGLU189
BHIS108
BHIS112
BGLU189

site_idSWS_FT_FI3
Number of Residues2
DetailsMOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291
ChainResidueDetails
CSER65
DSER65

site_idSWS_FT_FI4
Number of Residues2
DetailsMOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457
ChainResidueDetails
CTHR66
DTHR66

site_idSWS_FT_FI5
Number of Residues2
DetailsMOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742
ChainResidueDetails
CGLY76
DGLY76
BARG429
BASP895

site_idSWS_FT_FI6
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603
ChainResidueDetails
CLYS6
DLYS6
BLYS192
BLYS697

site_idSWS_FT_FI7
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
ChainResidueDetails
CGLY76
DGLY76

site_idSWS_FT_FI8
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144
ChainResidueDetails
CLYS11
CLYS48
DLYS11
DLYS48

site_idSWS_FT_FI9
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860
ChainResidueDetails
CLYS27
DLYS27

site_idSWS_FT_FI10
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127
ChainResidueDetails
CLYS29
DLYS29

site_idSWS_FT_FI11
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577
ChainResidueDetails
CLYS33
DLYS33

site_idSWS_FT_FI12
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106
ChainResidueDetails
CLYS63
DLYS63

218853

PDB entries from 2024-04-24

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