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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

2WDT

Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME

Functional Information from GO Data
ChainGOidnamespacecontents
A0000151cellular_componentubiquitin ligase complex
A0000338biological_processprotein deneddylation
A0004843molecular_functioncysteine-type deubiquitinase activity
A0005737cellular_componentcytoplasm
A0006508biological_processproteolysis
A0006511biological_processubiquitin-dependent protein catabolic process
A0008233molecular_functionpeptidase activity
A0008234molecular_functioncysteine-type peptidase activity
A0016579biological_processprotein deubiquitination
A0016787molecular_functionhydrolase activity
A0019784molecular_functiondeNEDDylase activity
A0030163biological_processprotein catabolic process
A0043130molecular_functionubiquitin binding
C0000151cellular_componentubiquitin ligase complex
C0000338biological_processprotein deneddylation
C0004843molecular_functioncysteine-type deubiquitinase activity
C0005737cellular_componentcytoplasm
C0006508biological_processproteolysis
C0006511biological_processubiquitin-dependent protein catabolic process
C0008233molecular_functionpeptidase activity
C0008234molecular_functioncysteine-type peptidase activity
C0016579biological_processprotein deubiquitination
C0016787molecular_functionhydrolase activity
C0019784molecular_functiondeNEDDylase activity
C0030163biological_processprotein catabolic process
C0043130molecular_functionubiquitin binding
Functional Information from PDB Data
site_idAC1
Number of Residues1
DetailsBINDING SITE FOR RESIDUE CL D 1076
ChainResidue
DARG42
site_idAC2
Number of Residues1
DetailsBINDING SITE FOR RESIDUE CL B 1076
ChainResidue
BARG42
Functional Information from PROSITE/UniProt
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 Residues12
DetailsRegion: {"description":"Interaction with ubiquitin","evidences":[{"source":"PubMed","id":"20042598","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues16
DetailsRegion: {"description":"Crossover loop which restricts access of large ubiquitin adducts to the active site","evidences":[{"source":"PubMed","id":"19047059","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues2
DetailsActive site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"20042598","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues2
DetailsActive site: {"description":"Proton donor","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues6
DetailsSite: {"description":"Interaction with ubiquitin","evidences":[{"source":"PubMed","id":"20042598","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues2
DetailsSite: {"description":"Transition state stabilizer","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsSite: {"description":"Important for enzyme activity","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues4
DetailsSite: {"description":"Interacts with activating enzyme"}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsSite: {"description":"Essential for function"}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues2
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_FI11
Number of Residues2
DetailsModified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI12
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"}]}
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":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18719106","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI14
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"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues2
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_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":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","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":"25752577","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idCSA1
Number of Residues4
DetailsAnnotated By Reference To The Literature 1uch
ChainResidueDetails
AASP179
AHIS164
ACYS92
AGLN86
site_idCSA2
Number of Residues4
DetailsAnnotated By Reference To The Literature 1uch
ChainResidueDetails
CASP179
CHIS164
CCYS92
CGLN86

243911

PDB entries from 2025-10-29

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