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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9K2W

Cryo-EM structure of USP7:DNMT1 complex; closed conformation

Functional Information from GO Data
ChainGOidnamespacecontents
A0002039molecular_functionp53 binding
A0004197molecular_functioncysteine-type endopeptidase activity
A0004843molecular_functioncysteine-type deubiquitinase activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005694cellular_componentchromosome
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006281biological_processDNA repair
A0006283biological_processtranscription-coupled nucleotide-excision repair
A0006307biological_processDNA alkylation repair
A0006508biological_processproteolysis
A0006974biological_processDNA damage response
A0008233molecular_functionpeptidase activity
A0008234molecular_functioncysteine-type peptidase activity
A0010803biological_processregulation of tumor necrosis factor-mediated signaling pathway
A0016567biological_processprotein ubiquitination
A0016579biological_processprotein deubiquitination
A0016604cellular_componentnuclear body
A0016605cellular_componentPML body
A0016787molecular_functionhydrolase activity
A0031647biological_processregulation of protein stability
A0032435biological_processnegative regulation of proteasomal ubiquitin-dependent protein catabolic process
A0032991cellular_componentprotein-containing complex
A0035520biological_processmonoubiquitinated protein deubiquitination
A0042752biological_processregulation of circadian rhythm
A0044027biological_processnegative regulation of gene expression via chromosomal CpG island methylation
A0045721biological_processnegative regulation of gluconeogenesis
A0048511biological_processrhythmic process
A0050821biological_processprotein stabilization
A0051090biological_processregulation of DNA-binding transcription factor activity
A0070203biological_processregulation of establishment of protein localization to telomere
A0075342biological_processsymbiont-mediated disruption of host cell PML body
A0101005molecular_functiondeubiquitinase activity
A0140374biological_processantiviral innate immune response
A1901796biological_processregulation of signal transduction by p53 class mediator
A1904262biological_processnegative regulation of TORC1 signaling
A1904353biological_processregulation of telomere capping
A1905279biological_processregulation of retrograde transport, endosome to Golgi
A1990380molecular_functionK48-linked deubiquitinase activity
B0003677molecular_functionDNA binding
B0003682molecular_functionchromatin binding
B0008168molecular_functionmethyltransferase activity
B0008270molecular_functionzinc ion binding
Functional Information from PROSITE/UniProt
site_idPS00094
Number of Residues13
DetailsC5_MTASE_1 C-5 cytosine-specific DNA methylases active site. EmLcgGpPCqGFS
ChainResidueDetails
BGLU1218-SER1230
site_idPS00095
Number of Residues19
DetailsC5_MTASE_2 C-5 cytosine-specific DNA methylases C-terminal signature. RqvGNAVpPpLakaIgleI
ChainResidueDetails
BARG1574-ILE1592
site_idPS00972
Number of Residues16
DetailsUSP_1 Ubiquitin specific protease (USP) domain signature 1. GLknqGAtCYMNSlLQ
ChainResidueDetails
AGLY215-GLN230
site_idPS00973
Number of Residues18
DetailsUSP_2 Ubiquitin specific protease (USP) domain signature 2. YiLhAVlvHsGdnhg..GHY
ChainResidueDetails
ATYR448-TYR465
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues179
DetailsRegion: {"description":"Interaction with ICP0/VMW110","evidences":[{"source":"PubMed","id":"16160161","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17651432","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"17651432","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues125
DetailsDomain: {"description":"BAH 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00370","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues460
DetailsDomain: {"description":"SAM-dependent MTase C5-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU01016","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues61
DetailsRegion: {"description":"Autoinhibitory linker"}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues30
DetailsRegion: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues10
DetailsCompositional bias: {"description":"Acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues12
DetailsCompositional bias: {"description":"Basic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues1
DetailsActive site: {}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues5
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00509","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"P13864","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"21163962","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3PTA","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues1
DetailsSite: {"description":"Important for activity","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P13864","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17081983","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI20
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18220336","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues7
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"21947282","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idMCSA1
Number of Residues
DetailsM-CSA 789
ChainResidueDetails

246905

PDB entries from 2025-12-31

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