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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

3I3T

Crystal structure of covalent ubiquitin-USP21 complex

Functional Information from GO Data
ChainGOidnamespacecontents
A0004843molecular_functioncysteine-type deubiquitinase activity
A0016579biological_processprotein deubiquitination
C0004843molecular_functioncysteine-type deubiquitinase activity
C0016579biological_processprotein deubiquitination
E0004843molecular_functioncysteine-type deubiquitinase activity
E0016579biological_processprotein deubiquitination
G0004843molecular_functioncysteine-type deubiquitinase activity
G0016579biological_processprotein deubiquitination
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 700
ChainResidue
ACYS384
ACYS387
ACYS437
ACYS440
site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN C 700
ChainResidue
CCYS384
CCYS387
CCYS437
CCYS440
site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN E 700
ChainResidue
ECYS387
ECYS437
ECYS440
ECYS384
site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN G 700
ChainResidue
GCYS384
GCYS387
GCYS437
GCYS440
site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE NEH B 76
ChainResidue
AASN219
ACYS221
AGLY517
BGLY75
site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NEH D 76
ChainResidue
CASN219
CCYS221
CGLN299
CGLY517
CHIS518
DGLY75
site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NEH F 76
ChainResidue
EASN219
ECYS221
EGLN299
EGLY517
FGLY75
site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NEH H 76
ChainResidue
GASN219
GCYS221
GGLN299
GGLY517
HGLY75
Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
BLYS27-ASP52
site_idPS00972
Number of Residues16
DetailsUSP_1 Ubiquitin specific protease (USP) domain signature 1. GLrnlGNtCFLNAvLQ
ChainResidueDetails
AGLY213-GLN228
site_idPS00973
Number of Residues18
DetailsUSP_2 Ubiquitin specific protease (USP) domain signature 2. YqLyALcnHsGsvhy..GHY
ChainResidueDetails
ATYR502-TYR519
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsActive site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"10799498","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"32011234","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues4
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU10092","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10093","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues16
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"21399617","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2Y5B","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues8
DetailsSite: {"description":"Interacts with activating enzyme"}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues4
DetailsSite: {"description":"Essential for function"}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
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_FI7
Number of Residues4
DetailsModified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues4
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_FI9
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":"18719106","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI10
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"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues4
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_FI12
Number of Residues4
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_FI13
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

246704

PDB entries from 2025-12-24

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