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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5YDK

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form

Functional Information from PDB Data
site_idAC1
Number of Residues7
Detailsbinding site for residue GOL J 101
ChainResidue
JMET1
JGLU16
JGLU18
JHOH208
LTYR145
LARG148
LGLU152
site_idAC2
Number of Residues7
Detailsbinding site for residue GOL C 101
ChainResidue
AGLU152
CMET1
CGLU16
CHOH207
CHOH210
ATYR145
AARG148
site_idAC3
Number of Residues14
Detailsbinding site for Di-peptide CYS G 190 and CYS F 190
ChainResidue
CARG72
FILE186
FASN187
FASN188
FPHE189
FGLU191
GILE186
GILE186
GASN187
GASN188
GPHE189
GGLU191
JARG72
JARG72
site_idAC4
Number of Residues15
Detailsbinding site for Di-peptide LYS I 63 and GLY H 76
ChainResidue
GGLU153
HMET1
HGLN62
HGLU64
HSER65
HLEU73
HGLY75
HHOH107
IMET1
IGLN2
IGLN62
IGLU64
ISER65
IHOH116
IHOH119
site_idAC5
Number of Residues12
Detailsbinding site for Di-peptide LYS J 63 and GLY K 76
ChainResidue
JGLN2
JGLN62
JGLU64
JSER65
JHOH214
KMET1
KGLN62
KGLU64
KSER65
KLEU73
KARG74
KGLY75
Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
BLYS27-ASP52
DLYS27-ASP52
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues92
DetailsRegion: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues32
DetailsMotif: {"description":"UMI motif","evidences":[{"source":"HAMAP-Rule","id":"MF_03066","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues92
DetailsMotif: {"description":"MIU motif 1","evidences":[{"source":"HAMAP-Rule","id":"MF_03066","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues300
DetailsDomain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues16
DetailsSite: {"description":"Interacts with activating enzyme"}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues8
DetailsSite: {"description":"Essential for function"}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues8
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_FI9
Number of Residues8
DetailsModified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues4
DetailsModified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"PubMed","id":"28525742","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues8
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_FI12
Number of Residues8
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues16
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_FI14
Number of Residues8
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_FI15
Number of Residues8
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_FI16
Number of Residues8
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_FI17
Number of Residues12
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

243911

PDB entries from 2025-10-29

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