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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9KHS

Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation)

Functional Information from GO Data
ChainGOidnamespacecontents
A0000209biological_processprotein polyubiquitination
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0006511biological_processubiquitin-dependent protein catabolic process
A0016567biological_processprotein ubiquitination
A0016740molecular_functiontransferase activity
A0031398biological_processpositive regulation of protein ubiquitination
A0034450molecular_functionubiquitin-ubiquitin ligase activity
A0036503biological_processERAD pathway
A0061630molecular_functionubiquitin protein ligase activity
A0070936biological_processprotein K48-linked ubiquitination
A0071361biological_processcellular response to ethanol
B0000166molecular_functionnucleotide binding
B0000209biological_processprotein polyubiquitination
B0004842molecular_functionubiquitin-protein transferase activity
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0006511biological_processubiquitin-dependent protein catabolic process
B0016567biological_processprotein ubiquitination
B0016740molecular_functiontransferase activity
B0030674molecular_functionprotein-macromolecule adaptor activity
B0034605biological_processcellular response to heat
B0043130molecular_functionubiquitin binding
B0043162biological_processubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
B0061631molecular_functionubiquitin conjugating enzyme activity
B0070628molecular_functionproteasome binding
B0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
B0072344biological_processrescue of stalled ribosome
B0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
B1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
Functional Information from PROSITE/UniProt
site_idPS00183
Number of Residues16
DetailsUBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNInan.GnICLdiL
ChainResidueDetails
BTYR75-LEU90
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
CLYS27-ASP52
ELYS27-ASP52
DLYS27-ASP52
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues146
DetailsDomain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues21
DetailsRegion: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues11
DetailsCompositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues1
DetailsActive site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues150
DetailsDomain: {"description":"Ubiquitin-like 9","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues75
DetailsDomain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsSite: {"description":"Interacts with activating enzyme"}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues1
DetailsSite: {"description":"Essential for function"}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"PubMed","id":"24660806","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24751536","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24784582","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25527291","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues1
DetailsModified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues1
DetailsModified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"PubMed","id":"28525742","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"15466860","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI20
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18719106","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues74
DetailsDomain: {"description":"U-box"}
ChainResidueDetails

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PDB entries from 2025-11-12

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