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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

3BY4

Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin

Functional Information from GO Data
ChainGOidnamespacecontents
A0004843molecular_functioncysteine-type deubiquitinase activity
A0016579biological_processprotein deubiquitination
A0030433biological_processubiquitin-dependent ERAD pathway
A0101005molecular_functiondeubiquitinase activity
Functional Information from PDB Data
site_idAC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE 3CN B 77
ChainResidue
AASP117
AASN118
ACYS120
ATRP175
AILE221
AHIS222
BGLY75
Functional Information from PROSITE/UniProt
site_idPS00028
Number of Residues23
DetailsZINC_FINGER_C2H2_1 Zinc finger C2H2 type domain signature. Cnt..CqmtFvgerevarHaestgH
ChainResidueDetails
ACYS272-HIS294
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
BLYS27-ASP52
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues120
DetailsDomain: {"description":"OTU","evidences":[{"source":"PROSITE-ProRule","id":"PRU00139","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues6
DetailsRegion: {"description":"Cys-loop","evidences":[{"source":"UniProtKB","id":"Q5VVQ6","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues10
DetailsRegion: {"description":"Variable-loop","evidences":[{"source":"UniProtKB","id":"Q5VVQ6","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues4
DetailsRegion: {"description":"His-loop","evidences":[{"source":"UniProtKB","id":"Q5VVQ6","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues5
DetailsRegion: {"description":"S2 site","evidences":[{"source":"UniProtKB","id":"Q5VVQ6","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues1
DetailsActive site: {"evidences":[{"source":"UniProtKB","id":"Q96FW1","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues1
DetailsActive site: {"description":"Nucleophile","evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues1
DetailsActive site: {"evidences":[{"source":"UniProtKB","id":"Q5VVQ6","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"Q5VVQ6","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI10
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_FI11
Number of Residues2
DetailsSite: {"description":"Interacts with activating enzyme"}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues1
DetailsSite: {"description":"Essential for function"}
ChainResidueDetails
site_idSWS_FT_FI13
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_FI14
Number of Residues1
DetailsModified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI15
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_FI16
Number of Residues2
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_FI17
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_FI18
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_FI19
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_FI20
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

246333

PDB entries from 2025-12-17

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