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5XIT

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

Functional Information from PDB Data
site_idAC1
Number of Residues1
Detailsbinding site for residue GOL D 101
ChainResidue
DLYS33

site_idAC2
Number of Residues5
Detailsbinding site for residue PR E 201
ChainResidue
AHOH314
AHOH319
EHOH306
EHOH308
HHOH104

site_idAC3
Number of Residues2
Detailsbinding site for residue PR E 203
ChainResidue
AARG117
AARG118

site_idAC4
Number of Residues1
Detailsbinding site for residue GOL E 204
ChainResidue
EARG118

site_idAC5
Number of Residues2
Detailsbinding site for residue GOL A 201
ChainResidue
APRO113
DTHR14

site_idAC6
Number of Residues5
Detailsbinding site for residue GOL A 202
ChainResidue
AGLU119
AGLU123
BASP32
BLYS33
DTHR9

site_idAC7
Number of Residues1
Detailsbinding site for residue GOL A 203
ChainResidue
AGLU137

Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
HLYS27-ASP52
DLYS27-ASP52

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues150
DetailsDomain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues8
DetailsSite: {"description":"Interacts with activating enzyme"}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues4
DetailsSite: {"description":"Essential for function"}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"UniProtKB","id":"P62979","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues2
DetailsModified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"UniProtKB","id":"P62979","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues30
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P62979","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues46
DetailsRegion: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues16
DetailsMotif: {"description":"UMI motif","evidences":[{"source":"HAMAP-Rule","id":"MF_03066","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

246031

PDB entries from 2025-12-10

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